diff --git a/Glycogen/code/Gen5-20260123-mgig-glycogenglo.Rmd b/Glycogen/code/Gen5-20260123-mgig-glycogenglo.Rmd index f21b158..5a2912f 100644 --- a/Glycogen/code/Gen5-20260123-mgig-glycogenglo.Rmd +++ b/Glycogen/code/Gen5-20260123-mgig-glycogenglo.Rmd @@ -26,6 +26,16 @@ knitr::opts_chunk$set( plate_layout <- read.csv("https://raw.githubusercontent.com/RobertsLab/sormi-assay-development/refs/heads/main/Glycogen/data/raw_luminescence/layout-Gen5-20260123-mgig-glycogenglo.csv", header = FALSE) raw_luminescence <- read.csv("https://raw.githubusercontent.com/RobertsLab/sormi-assay-development/refs/heads/main/Glycogen/data/raw_luminescence/raw_lum-Gen5-20260123-mgig-glycogenglo.csv", header = FALSE) +tissue_weights <- read.csv("https://raw.githubusercontent.com/RobertsLab/sormi-assay-development/refs/heads/main/Glycogen/data/20251210-mgig-ctenidia_weights-glycogen_assay.csv") + +# Homogenate volume (µL): 750 µL PBS/HCl + 250 µL TRIS buffer = 1000 µL total +homogenate_volume_uL <- 1000 + +# Helper function to extract tissue weight from plate layout label +# Label format: "---df.", e.g., "A1-glyc-25-df.2" +get_weight_from_label <- function(label) { + as.numeric(gsub("^[^-]+-[a-z]+-([0-9.]+)-df.*", "\\1", as.character(label))) +} cat("Plate layout:\n") str(plate_layout) @@ -579,17 +589,28 @@ for (i in 1:nrow(glycogen_summary_data)) { ```{r, sample glycogen calculations} -tab <- matrix(c(glyc_A1_dilution, glyc_A1_mean_lum, glyc_A1_mean_conc, (glyc_A1_dilution*glyc_A1_mean_conc), - glyc_A2_dilution, glyc_A2_mean_lum, glyc_A2_mean_conc, (glyc_A2_dilution*glyc_A2_mean_conc), - glyc_A3_dilution, glyc_A3_mean_lum, glyc_A3_mean_conc, (glyc_A3_dilution*glyc_A3_mean_conc), - glyc_A4_dilution, glyc_A4_mean_lum, glyc_A4_mean_conc, (glyc_A4_dilution*glyc_A4_mean_conc), - glyc_A5_dilution, glyc_A5_mean_lum, glyc_A5_mean_conc, (glyc_A5_dilution*glyc_A5_mean_conc), - glyc_A6_dilution, glyc_A6_mean_lum, glyc_A6_mean_conc, (glyc_A6_dilution*glyc_A6_mean_conc), - glyc_A7_dilution, glyc_A7_mean_lum, glyc_A7_mean_conc, (glyc_A7_dilution*glyc_A7_mean_conc), - glyc_A8_dilution, glyc_A8_mean_lum, glyc_A8_mean_conc, (glyc_A8_dilution*glyc_A8_mean_conc), - glyc_B1_dilution, glyc_B1_mean_lum, glyc_B1_mean_conc, (glyc_B1_dilution*glyc_B1_mean_conc), - glyc_B2_dilution, glyc_B2_mean_lum, glyc_B2_mean_conc, (glyc_B2_dilution*glyc_B2_mean_conc)), ncol=4, byrow=TRUE) -colnames(tab) <- c('Dilution factor','Luminescence','Calculated Glycogen (ug/uL)', 'Total glycogen (ug/uL)') +wt_A1 <- get_weight_from_label(plate_layout[1, 1]) +wt_A2 <- get_weight_from_label(plate_layout[2, 1]) +wt_A3 <- get_weight_from_label(plate_layout[3, 1]) +wt_A4 <- get_weight_from_label(plate_layout[4, 1]) +wt_A5 <- get_weight_from_label(plate_layout[5, 1]) +wt_A6 <- get_weight_from_label(plate_layout[1, 4]) +wt_A7 <- get_weight_from_label(plate_layout[2, 4]) +wt_A8 <- get_weight_from_label(plate_layout[3, 4]) +wt_B1 <- get_weight_from_label(plate_layout[4, 4]) +wt_B2 <- get_weight_from_label(plate_layout[5, 4]) + +tab <- matrix(c(glyc_A1_dilution, glyc_A1_mean_lum, glyc_A1_mean_conc, (glyc_A1_dilution*glyc_A1_mean_conc), (glyc_A1_dilution*glyc_A1_mean_conc*homogenate_volume_uL)/wt_A1, + glyc_A2_dilution, glyc_A2_mean_lum, glyc_A2_mean_conc, (glyc_A2_dilution*glyc_A2_mean_conc), (glyc_A2_dilution*glyc_A2_mean_conc*homogenate_volume_uL)/wt_A2, + glyc_A3_dilution, glyc_A3_mean_lum, glyc_A3_mean_conc, (glyc_A3_dilution*glyc_A3_mean_conc), (glyc_A3_dilution*glyc_A3_mean_conc*homogenate_volume_uL)/wt_A3, + glyc_A4_dilution, glyc_A4_mean_lum, glyc_A4_mean_conc, (glyc_A4_dilution*glyc_A4_mean_conc), (glyc_A4_dilution*glyc_A4_mean_conc*homogenate_volume_uL)/wt_A4, + glyc_A5_dilution, glyc_A5_mean_lum, glyc_A5_mean_conc, (glyc_A5_dilution*glyc_A5_mean_conc), (glyc_A5_dilution*glyc_A5_mean_conc*homogenate_volume_uL)/wt_A5, + glyc_A6_dilution, glyc_A6_mean_lum, glyc_A6_mean_conc, (glyc_A6_dilution*glyc_A6_mean_conc), (glyc_A6_dilution*glyc_A6_mean_conc*homogenate_volume_uL)/wt_A6, + glyc_A7_dilution, glyc_A7_mean_lum, glyc_A7_mean_conc, (glyc_A7_dilution*glyc_A7_mean_conc), (glyc_A7_dilution*glyc_A7_mean_conc*homogenate_volume_uL)/wt_A7, + glyc_A8_dilution, glyc_A8_mean_lum, glyc_A8_mean_conc, (glyc_A8_dilution*glyc_A8_mean_conc), (glyc_A8_dilution*glyc_A8_mean_conc*homogenate_volume_uL)/wt_A8, + glyc_B1_dilution, glyc_B1_mean_lum, glyc_B1_mean_conc, (glyc_B1_dilution*glyc_B1_mean_conc), (glyc_B1_dilution*glyc_B1_mean_conc*homogenate_volume_uL)/wt_B1, + glyc_B2_dilution, glyc_B2_mean_lum, glyc_B2_mean_conc, (glyc_B2_dilution*glyc_B2_mean_conc), (glyc_B2_dilution*glyc_B2_mean_conc*homogenate_volume_uL)/wt_B2), ncol=5, byrow=TRUE) +colnames(tab) <- c('Dilution factor','Luminescence','Calculated Glycogen (ug/uL)', 'Total glycogen (ug/uL)', 'Normalized glycogen (ug/mg tissue)') rownames(tab) <- c('A1','A2','A3','A4','A5','A6','A7','A8','B1','B2' ) tab <- as.table(tab) tab @@ -1136,17 +1157,17 @@ for (i in 1:nrow(glucose_summary_data)) { ```{r, sample glucose calculations} -tab <- matrix(c(glu_A1_dilution, glu_A1_mean_lum, glu_A1_mean_conc, (glu_A1_dilution*glu_A1_mean_conc), - glu_A2_dilution, glu_A2_mean_lum, glu_A2_mean_conc, (glu_A2_dilution*glu_A2_mean_conc), - glu_A3_dilution, glu_A3_mean_lum, glu_A3_mean_conc, (glu_A3_dilution*glu_A3_mean_conc), - glu_A4_dilution, glu_A4_mean_lum, glu_A4_mean_conc, (glu_A4_dilution*glu_A4_mean_conc), - glu_A5_dilution, glu_A5_mean_lum, glu_A5_mean_conc, (glu_A5_dilution*glu_A5_mean_conc), - glu_A6_dilution, glu_A6_mean_lum, glu_A6_mean_conc, (glu_A6_dilution*glu_A6_mean_conc), - glu_A7_dilution, glu_A7_mean_lum, glu_A7_mean_conc, (glu_A7_dilution*glu_A7_mean_conc), - glu_A8_dilution, glu_A8_mean_lum, glu_A8_mean_conc, (glu_A8_dilution*glu_A8_mean_conc), - glu_B1_dilution, glu_B1_mean_lum, glu_B1_mean_conc, (glu_B1_dilution*glu_B1_mean_conc), - glu_B2_dilution, glu_B2_mean_lum, glu_B2_mean_conc, (glu_B2_dilution*glu_B2_mean_conc)), ncol=4, byrow=TRUE) -colnames(tab) <- c('Dilution factor','Luminescence','Calculated glucose (uM)', 'Total glucose (uM)') +tab <- matrix(c(glu_A1_dilution, glu_A1_mean_lum, glu_A1_mean_conc, (glu_A1_dilution*glu_A1_mean_conc), (glu_A1_dilution*glu_A1_mean_conc*homogenate_volume_uL)/wt_A1, + glu_A2_dilution, glu_A2_mean_lum, glu_A2_mean_conc, (glu_A2_dilution*glu_A2_mean_conc), (glu_A2_dilution*glu_A2_mean_conc*homogenate_volume_uL)/wt_A2, + glu_A3_dilution, glu_A3_mean_lum, glu_A3_mean_conc, (glu_A3_dilution*glu_A3_mean_conc), (glu_A3_dilution*glu_A3_mean_conc*homogenate_volume_uL)/wt_A3, + glu_A4_dilution, glu_A4_mean_lum, glu_A4_mean_conc, (glu_A4_dilution*glu_A4_mean_conc), (glu_A4_dilution*glu_A4_mean_conc*homogenate_volume_uL)/wt_A4, + glu_A5_dilution, glu_A5_mean_lum, glu_A5_mean_conc, (glu_A5_dilution*glu_A5_mean_conc), (glu_A5_dilution*glu_A5_mean_conc*homogenate_volume_uL)/wt_A5, + glu_A6_dilution, glu_A6_mean_lum, glu_A6_mean_conc, (glu_A6_dilution*glu_A6_mean_conc), (glu_A6_dilution*glu_A6_mean_conc*homogenate_volume_uL)/wt_A6, + glu_A7_dilution, glu_A7_mean_lum, glu_A7_mean_conc, (glu_A7_dilution*glu_A7_mean_conc), (glu_A7_dilution*glu_A7_mean_conc*homogenate_volume_uL)/wt_A7, + glu_A8_dilution, glu_A8_mean_lum, glu_A8_mean_conc, (glu_A8_dilution*glu_A8_mean_conc), (glu_A8_dilution*glu_A8_mean_conc*homogenate_volume_uL)/wt_A8, + glu_B1_dilution, glu_B1_mean_lum, glu_B1_mean_conc, (glu_B1_dilution*glu_B1_mean_conc), (glu_B1_dilution*glu_B1_mean_conc*homogenate_volume_uL)/wt_B1, + glu_B2_dilution, glu_B2_mean_lum, glu_B2_mean_conc, (glu_B2_dilution*glu_B2_mean_conc), (glu_B2_dilution*glu_B2_mean_conc*homogenate_volume_uL)/wt_B2), ncol=5, byrow=TRUE) +colnames(tab) <- c('Dilution factor','Luminescence','Calculated glucose (ug/uL)', 'Total glucose (ug/uL)', 'Normalized glucose (ug/mg tissue)') rownames(tab) <- c('A1','A2','A3','A4','A5','A6','A7','A8','B1','B2' ) tab <- as.table(tab) tab diff --git a/Glycogen/code/Gen5-20260126-mgig-glycogenglo.Rmd b/Glycogen/code/Gen5-20260126-mgig-glycogenglo.Rmd index c7c5ab3..711af57 100644 --- a/Glycogen/code/Gen5-20260126-mgig-glycogenglo.Rmd +++ b/Glycogen/code/Gen5-20260126-mgig-glycogenglo.Rmd @@ -26,6 +26,16 @@ knitr::opts_chunk$set( plate_layout <- read.csv("https://raw.githubusercontent.com/RobertsLab/sormi-assay-development/refs/heads/main/Glycogen/data/raw_luminescence/layout-Gen5-20260126-mgig-glycogenglo.csv", header = FALSE) raw_luminescence <- read.csv("https://raw.githubusercontent.com/RobertsLab/sormi-assay-development/refs/heads/main/Glycogen/data/raw_luminescence/raw_lum-Gen5-20260126-mgig-glycogenglo.csv", header = FALSE) +tissue_weights <- read.csv("https://raw.githubusercontent.com/RobertsLab/sormi-assay-development/refs/heads/main/Glycogen/data/20251210-mgig-ctenidia_weights-glycogen_assay.csv") + +# Homogenate volume (µL): 750 µL PBS/HCl + 250 µL TRIS buffer = 1000 µL total +homogenate_volume_uL <- 1000 + +# Helper function to extract tissue weight from plate layout label +# Label format: "---df.", e.g., "A1-glyc-25-df.2" +get_weight_from_label <- function(label) { + as.numeric(gsub("^[^-]+-[a-z]+-([0-9.]+)-df.*", "\\1", as.character(label))) +} cat("Plate layout:\n") str(plate_layout) @@ -587,17 +597,23 @@ for (i in 1:nrow(glycogen_summary_data)) { ```{r, sample glycogen calculations} -tab <- matrix(c(glyc_A1_dilution2, glyc_A1_mean_lum2, glyc_A1_mean_conc2, (glyc_A1_dilution2*glyc_A1_mean_conc2), - glyc_A2_dilution2, glyc_A2_mean_lum2, glyc_A2_mean_conc2, (glyc_A2_dilution2*glyc_A2_mean_conc2), - glyc_A3_dilution2, glyc_A3_mean_lum2, glyc_A3_mean_conc2, (glyc_A3_dilution2*glyc_A3_mean_conc2), - glyc_A4_dilution2, glyc_A4_mean_lum2, glyc_A4_mean_conc2, (glyc_A4_dilution2*glyc_A4_mean_conc2), - glyc_A5_dilution2, glyc_A5_mean_lum2, glyc_A5_mean_conc2, (glyc_A5_dilution2*glyc_A5_mean_conc2), - glyc_A1_dilution4, glyc_A1_mean_lum4, glyc_A1_mean_conc4, (glyc_A1_dilution4*glyc_A1_mean_conc4), - glyc_A2_dilution4, glyc_A2_mean_lum4, glyc_A2_mean_conc4, (glyc_A2_dilution4*glyc_A2_mean_conc4), - glyc_A3_dilution4, glyc_A3_mean_lum4, glyc_A3_mean_conc4, (glyc_A3_dilution4*glyc_A3_mean_conc4), - glyc_A4_dilution4, glyc_A4_mean_lum4, glyc_A4_mean_conc4, (glyc_A4_dilution4*glyc_A4_mean_conc4), - glyc_A5_dilution4, glyc_A5_mean_lum4, glyc_A5_mean_conc4, (glyc_A5_dilution4*glyc_A5_mean_conc4)), ncol=4, byrow=TRUE) -colnames(tab) <- c('Dilution factor','Luminescence','Calculated Glycogen (ug/uL)', 'Total glycogen (ug/uL)') +wt_A1 <- get_weight_from_label(plate_layout[1, 1]) +wt_A2 <- get_weight_from_label(plate_layout[2, 1]) +wt_A3 <- get_weight_from_label(plate_layout[3, 1]) +wt_A4 <- get_weight_from_label(plate_layout[4, 1]) +wt_A5 <- get_weight_from_label(plate_layout[5, 1]) + +tab <- matrix(c(glyc_A1_dilution2, glyc_A1_mean_lum2, glyc_A1_mean_conc2, (glyc_A1_dilution2*glyc_A1_mean_conc2), (glyc_A1_dilution2*glyc_A1_mean_conc2*homogenate_volume_uL)/wt_A1, + glyc_A2_dilution2, glyc_A2_mean_lum2, glyc_A2_mean_conc2, (glyc_A2_dilution2*glyc_A2_mean_conc2), (glyc_A2_dilution2*glyc_A2_mean_conc2*homogenate_volume_uL)/wt_A2, + glyc_A3_dilution2, glyc_A3_mean_lum2, glyc_A3_mean_conc2, (glyc_A3_dilution2*glyc_A3_mean_conc2), (glyc_A3_dilution2*glyc_A3_mean_conc2*homogenate_volume_uL)/wt_A3, + glyc_A4_dilution2, glyc_A4_mean_lum2, glyc_A4_mean_conc2, (glyc_A4_dilution2*glyc_A4_mean_conc2), (glyc_A4_dilution2*glyc_A4_mean_conc2*homogenate_volume_uL)/wt_A4, + glyc_A5_dilution2, glyc_A5_mean_lum2, glyc_A5_mean_conc2, (glyc_A5_dilution2*glyc_A5_mean_conc2), (glyc_A5_dilution2*glyc_A5_mean_conc2*homogenate_volume_uL)/wt_A5, + glyc_A1_dilution4, glyc_A1_mean_lum4, glyc_A1_mean_conc4, (glyc_A1_dilution4*glyc_A1_mean_conc4), (glyc_A1_dilution4*glyc_A1_mean_conc4*homogenate_volume_uL)/wt_A1, + glyc_A2_dilution4, glyc_A2_mean_lum4, glyc_A2_mean_conc4, (glyc_A2_dilution4*glyc_A2_mean_conc4), (glyc_A2_dilution4*glyc_A2_mean_conc4*homogenate_volume_uL)/wt_A2, + glyc_A3_dilution4, glyc_A3_mean_lum4, glyc_A3_mean_conc4, (glyc_A3_dilution4*glyc_A3_mean_conc4), (glyc_A3_dilution4*glyc_A3_mean_conc4*homogenate_volume_uL)/wt_A3, + glyc_A4_dilution4, glyc_A4_mean_lum4, glyc_A4_mean_conc4, (glyc_A4_dilution4*glyc_A4_mean_conc4), (glyc_A4_dilution4*glyc_A4_mean_conc4*homogenate_volume_uL)/wt_A4, + glyc_A5_dilution4, glyc_A5_mean_lum4, glyc_A5_mean_conc4, (glyc_A5_dilution4*glyc_A5_mean_conc4), (glyc_A5_dilution4*glyc_A5_mean_conc4*homogenate_volume_uL)/wt_A5), ncol=5, byrow=TRUE) +colnames(tab) <- c('Dilution factor','Luminescence','Calculated Glycogen (ug/uL)', 'Total glycogen (ug/uL)', 'Normalized glycogen (ug/mg tissue)') rownames(tab) <- c('A1.df2','A2.df2','A3.df2','A4.df2','A5.df2','A1.df4','A2.df4','A3.df4','A4.df4','Af.df4' ) tab <- as.table(tab) tab @@ -1149,17 +1165,17 @@ for (i in 1:nrow(glucose_summary_data)) { ```{r, sample glucose calculations} -tab <- matrix(c(glu_A1_dilution2, glu_A1_mean_lum2, glu_A1_mean_conc2, (glu_A1_dilution2*glu_A1_mean_conc2), - glu_A2_dilution2, glu_A2_mean_lum2, glu_A2_mean_conc2, (glu_A2_dilution2*glu_A2_mean_conc2), - glu_A3_dilution2, glu_A3_mean_lum2, glu_A3_mean_conc2, (glu_A3_dilution2*glu_A3_mean_conc2), - glu_A4_dilution2, glu_A4_mean_lum2, glu_A4_mean_conc2, (glu_A4_dilution2*glu_A4_mean_conc2), - glu_A5_dilution2, glu_A5_mean_lum2, glu_A5_mean_conc2, (glu_A5_dilution2*glu_A5_mean_conc2), - glu_A1_dilution4, glu_A1_mean_lum4, glu_A1_mean_conc4, (glu_A1_dilution4*glu_A1_mean_conc4), - glu_A2_dilution4, glu_A2_mean_lum4, glu_A2_mean_conc4, (glu_A2_dilution4*glu_A2_mean_conc4), - glu_A3_dilution4, glu_A3_mean_lum4, glu_A3_mean_conc4, (glu_A3_dilution4*glu_A3_mean_conc4), - glu_A4_dilution4, glu_A4_mean_lum4, glu_A4_mean_conc4, (glu_A4_dilution4*glu_A4_mean_conc4), - glu_A5_dilution4, glu_A5_mean_lum4, glu_A5_mean_conc4, (glu_A5_dilution4*glu_A5_mean_conc4)), ncol=4, byrow=TRUE) -colnames(tab) <- c('Dilution factor','Luminescence','Calculated Glycogen (ug/uL)', 'Total glucose (ug/uL)') +tab <- matrix(c(glu_A1_dilution2, glu_A1_mean_lum2, glu_A1_mean_conc2, (glu_A1_dilution2*glu_A1_mean_conc2), (glu_A1_dilution2*glu_A1_mean_conc2*homogenate_volume_uL)/wt_A1, + glu_A2_dilution2, glu_A2_mean_lum2, glu_A2_mean_conc2, (glu_A2_dilution2*glu_A2_mean_conc2), (glu_A2_dilution2*glu_A2_mean_conc2*homogenate_volume_uL)/wt_A2, + glu_A3_dilution2, glu_A3_mean_lum2, glu_A3_mean_conc2, (glu_A3_dilution2*glu_A3_mean_conc2), (glu_A3_dilution2*glu_A3_mean_conc2*homogenate_volume_uL)/wt_A3, + glu_A4_dilution2, glu_A4_mean_lum2, glu_A4_mean_conc2, (glu_A4_dilution2*glu_A4_mean_conc2), (glu_A4_dilution2*glu_A4_mean_conc2*homogenate_volume_uL)/wt_A4, + glu_A5_dilution2, glu_A5_mean_lum2, glu_A5_mean_conc2, (glu_A5_dilution2*glu_A5_mean_conc2), (glu_A5_dilution2*glu_A5_mean_conc2*homogenate_volume_uL)/wt_A5, + glu_A1_dilution4, glu_A1_mean_lum4, glu_A1_mean_conc4, (glu_A1_dilution4*glu_A1_mean_conc4), (glu_A1_dilution4*glu_A1_mean_conc4*homogenate_volume_uL)/wt_A1, + glu_A2_dilution4, glu_A2_mean_lum4, glu_A2_mean_conc4, (glu_A2_dilution4*glu_A2_mean_conc4), (glu_A2_dilution4*glu_A2_mean_conc4*homogenate_volume_uL)/wt_A2, + glu_A3_dilution4, glu_A3_mean_lum4, glu_A3_mean_conc4, (glu_A3_dilution4*glu_A3_mean_conc4), (glu_A3_dilution4*glu_A3_mean_conc4*homogenate_volume_uL)/wt_A3, + glu_A4_dilution4, glu_A4_mean_lum4, glu_A4_mean_conc4, (glu_A4_dilution4*glu_A4_mean_conc4), (glu_A4_dilution4*glu_A4_mean_conc4*homogenate_volume_uL)/wt_A4, + glu_A5_dilution4, glu_A5_mean_lum4, glu_A5_mean_conc4, (glu_A5_dilution4*glu_A5_mean_conc4), (glu_A5_dilution4*glu_A5_mean_conc4*homogenate_volume_uL)/wt_A5), ncol=5, byrow=TRUE) +colnames(tab) <- c('Dilution factor','Luminescence','Calculated glucose (ug/uL)', 'Total glucose (ug/uL)', 'Normalized glucose (ug/mg tissue)') rownames(tab) <- c('A1.df2','A2.df2','A3.df2','A4.df2','A5.df2','A1.df4','A2.df4','A3.df4','A4.df4','Af.df4' ) tab <- as.table(tab) tab diff --git a/Glycogen/code/Gen5-20260130-mgig-glycogenglo.Rmd b/Glycogen/code/Gen5-20260130-mgig-glycogenglo.Rmd index 9ec5e09..541ce5b 100644 --- a/Glycogen/code/Gen5-20260130-mgig-glycogenglo.Rmd +++ b/Glycogen/code/Gen5-20260130-mgig-glycogenglo.Rmd @@ -26,6 +26,16 @@ knitr::opts_chunk$set( plate_layout <- read.csv("https://raw.githubusercontent.com/RobertsLab/sormi-assay-development/refs/heads/main/Glycogen/data/raw_luminescence/layout-Gen5-20260130-mgig-glycogenglo.csv", header = FALSE) raw_luminescence <- read.csv("https://raw.githubusercontent.com/RobertsLab/sormi-assay-development/refs/heads/main/Glycogen/data/raw_luminescence/raw_lum-Gen5-20260130-mgig-glycogenglo.csv", header = FALSE) +tissue_weights <- read.csv("https://raw.githubusercontent.com/RobertsLab/sormi-assay-development/refs/heads/main/Glycogen/data/20251210-mgig-ctenidia_weights-glycogen_assay.csv") + +# Homogenate volume (µL): 750 µL PBS/HCl + 250 µL TRIS buffer = 1000 µL total +homogenate_volume_uL <- 1000 + +# Helper function to extract tissue weight from plate layout label +# Label format: "---df.", e.g., "A1-glyc-25-df.20" +get_weight_from_label <- function(label) { + as.numeric(gsub("^[^-]+-[a-z]+-([0-9.]+)-df.*", "\\1", as.character(label))) +} cat("Plate layout:\n") str(plate_layout) @@ -590,17 +600,23 @@ for (i in 1:nrow(glycogen_summary_data)) { ```{r, sample glycogen calculations} -tab <- matrix(c(glyc_A1_dilution20, glyc_A1_mean_lum20, glyc_A1_mean_conc20, (glyc_A1_dilution20*glyc_A1_mean_conc20), - glyc_A2_dilution20, glyc_A2_mean_lum20, glyc_A2_mean_conc20, (glyc_A2_dilution20*glyc_A2_mean_conc20), - glyc_A3_dilution20, glyc_A3_mean_lum20, glyc_A3_mean_conc20, (glyc_A3_dilution20*glyc_A3_mean_conc20), - glyc_A4_dilution20, glyc_A4_mean_lum20, glyc_A4_mean_conc20, (glyc_A4_dilution20*glyc_A4_mean_conc20), - glyc_A5_dilution20, glyc_A5_mean_lum20, glyc_A5_mean_conc20, (glyc_A5_dilution20*glyc_A5_mean_conc20), - glyc_A1_dilution100, glyc_A1_mean_lum100, glyc_A1_mean_conc100, (glyc_A1_dilution100*glyc_A1_mean_conc100), - glyc_A2_dilution100, glyc_A2_mean_lum100, glyc_A2_mean_conc100, (glyc_A2_dilution100*glyc_A2_mean_conc100), - glyc_A3_dilution100, glyc_A3_mean_lum100, glyc_A3_mean_conc100, (glyc_A3_dilution100*glyc_A3_mean_conc100), - glyc_A4_dilution100, glyc_A4_mean_lum100, glyc_A4_mean_conc100, (glyc_A4_dilution100*glyc_A4_mean_conc100), - glyc_A5_dilution100, glyc_A5_mean_lum100, glyc_A5_mean_conc100, (glyc_A5_dilution100*glyc_A5_mean_conc100)), ncol=4, byrow=TRUE) -colnames(tab) <- c('Dilution factor','Luminescence','Calculated Glycogen (ug/uL)', 'Total glycogen (ug/uL)') +wt_A1 <- get_weight_from_label(plate_layout[1, 1]) +wt_A2 <- get_weight_from_label(plate_layout[2, 1]) +wt_A3 <- get_weight_from_label(plate_layout[3, 1]) +wt_A4 <- get_weight_from_label(plate_layout[4, 1]) +wt_A5 <- get_weight_from_label(plate_layout[5, 1]) + +tab <- matrix(c(glyc_A1_dilution20, glyc_A1_mean_lum20, glyc_A1_mean_conc20, (glyc_A1_dilution20*glyc_A1_mean_conc20), (glyc_A1_dilution20*glyc_A1_mean_conc20*homogenate_volume_uL)/wt_A1, + glyc_A2_dilution20, glyc_A2_mean_lum20, glyc_A2_mean_conc20, (glyc_A2_dilution20*glyc_A2_mean_conc20), (glyc_A2_dilution20*glyc_A2_mean_conc20*homogenate_volume_uL)/wt_A2, + glyc_A3_dilution20, glyc_A3_mean_lum20, glyc_A3_mean_conc20, (glyc_A3_dilution20*glyc_A3_mean_conc20), (glyc_A3_dilution20*glyc_A3_mean_conc20*homogenate_volume_uL)/wt_A3, + glyc_A4_dilution20, glyc_A4_mean_lum20, glyc_A4_mean_conc20, (glyc_A4_dilution20*glyc_A4_mean_conc20), (glyc_A4_dilution20*glyc_A4_mean_conc20*homogenate_volume_uL)/wt_A4, + glyc_A5_dilution20, glyc_A5_mean_lum20, glyc_A5_mean_conc20, (glyc_A5_dilution20*glyc_A5_mean_conc20), (glyc_A5_dilution20*glyc_A5_mean_conc20*homogenate_volume_uL)/wt_A5, + glyc_A1_dilution100, glyc_A1_mean_lum100, glyc_A1_mean_conc100, (glyc_A1_dilution100*glyc_A1_mean_conc100), (glyc_A1_dilution100*glyc_A1_mean_conc100*homogenate_volume_uL)/wt_A1, + glyc_A2_dilution100, glyc_A2_mean_lum100, glyc_A2_mean_conc100, (glyc_A2_dilution100*glyc_A2_mean_conc100), (glyc_A2_dilution100*glyc_A2_mean_conc100*homogenate_volume_uL)/wt_A2, + glyc_A3_dilution100, glyc_A3_mean_lum100, glyc_A3_mean_conc100, (glyc_A3_dilution100*glyc_A3_mean_conc100), (glyc_A3_dilution100*glyc_A3_mean_conc100*homogenate_volume_uL)/wt_A3, + glyc_A4_dilution100, glyc_A4_mean_lum100, glyc_A4_mean_conc100, (glyc_A4_dilution100*glyc_A4_mean_conc100), (glyc_A4_dilution100*glyc_A4_mean_conc100*homogenate_volume_uL)/wt_A4, + glyc_A5_dilution100, glyc_A5_mean_lum100, glyc_A5_mean_conc100, (glyc_A5_dilution100*glyc_A5_mean_conc100), (glyc_A5_dilution100*glyc_A5_mean_conc100*homogenate_volume_uL)/wt_A5), ncol=5, byrow=TRUE) +colnames(tab) <- c('Dilution factor','Luminescence','Calculated Glycogen (ug/uL)', 'Total glycogen (ug/uL)', 'Normalized glycogen (ug/mg tissue)') rownames(tab) <- c('A1.df20','A2.df20','A3.df20','A4.df20','A5.df20','A1.df100','A2.df100','A3.df100','A4.df100','Af.df100') tab <- as.table(tab) tab @@ -1155,17 +1171,17 @@ for (i in 1:nrow(glucose_summary_data)) { ```{r, sample glucose calculations} -tab <- matrix(c(glu_A1_dilution20, glu_A1_mean_lum20, glu_A1_mean_conc20, (glu_A1_dilution20*glu_A1_mean_conc20), - glu_A2_dilution20, glu_A2_mean_lum20, glu_A2_mean_conc20, (glu_A2_dilution20*glu_A2_mean_conc20), - glu_A3_dilution20, glu_A3_mean_lum20, glu_A3_mean_conc20, (glu_A3_dilution20*glu_A3_mean_conc20), - glu_A4_dilution20, glu_A4_mean_lum20, glu_A4_mean_conc20, (glu_A4_dilution20*glu_A4_mean_conc20), - glu_A5_dilution20, glu_A5_mean_lum20, glu_A5_mean_conc20, (glu_A5_dilution20*glu_A5_mean_conc20), - glu_A1_dilution100, glu_A1_mean_lum100, glu_A1_mean_conc100, (glu_A1_dilution100*glu_A1_mean_conc100), - glu_A2_dilution100, glu_A2_mean_lum100, glu_A2_mean_conc100, (glu_A2_dilution100*glu_A2_mean_conc100), - glu_A3_dilution100, glu_A3_mean_lum100, glu_A3_mean_conc100, (glu_A3_dilution100*glu_A3_mean_conc100), - glu_A4_dilution100, glu_A4_mean_lum100, glu_A4_mean_conc100, (glu_A4_dilution100*glu_A4_mean_conc100), - glu_A5_dilution100, glu_A5_mean_lum100, glu_A5_mean_conc100, (glu_A5_dilution100*glu_A5_mean_conc100)), ncol=4, byrow=TRUE) -colnames(tab) <- c('Dilution factor','Luminescence','Calculated Glycogen (ug/uL)', 'Total glucose (ug/uL)') +tab <- matrix(c(glu_A1_dilution20, glu_A1_mean_lum20, glu_A1_mean_conc20, (glu_A1_dilution20*glu_A1_mean_conc20), (glu_A1_dilution20*glu_A1_mean_conc20*homogenate_volume_uL)/wt_A1, + glu_A2_dilution20, glu_A2_mean_lum20, glu_A2_mean_conc20, (glu_A2_dilution20*glu_A2_mean_conc20), (glu_A2_dilution20*glu_A2_mean_conc20*homogenate_volume_uL)/wt_A2, + glu_A3_dilution20, glu_A3_mean_lum20, glu_A3_mean_conc20, (glu_A3_dilution20*glu_A3_mean_conc20), (glu_A3_dilution20*glu_A3_mean_conc20*homogenate_volume_uL)/wt_A3, + glu_A4_dilution20, glu_A4_mean_lum20, glu_A4_mean_conc20, (glu_A4_dilution20*glu_A4_mean_conc20), (glu_A4_dilution20*glu_A4_mean_conc20*homogenate_volume_uL)/wt_A4, + glu_A5_dilution20, glu_A5_mean_lum20, glu_A5_mean_conc20, (glu_A5_dilution20*glu_A5_mean_conc20), (glu_A5_dilution20*glu_A5_mean_conc20*homogenate_volume_uL)/wt_A5, + glu_A1_dilution100, glu_A1_mean_lum100, glu_A1_mean_conc100, (glu_A1_dilution100*glu_A1_mean_conc100), (glu_A1_dilution100*glu_A1_mean_conc100*homogenate_volume_uL)/wt_A1, + glu_A2_dilution100, glu_A2_mean_lum100, glu_A2_mean_conc100, (glu_A2_dilution100*glu_A2_mean_conc100), (glu_A2_dilution100*glu_A2_mean_conc100*homogenate_volume_uL)/wt_A2, + glu_A3_dilution100, glu_A3_mean_lum100, glu_A3_mean_conc100, (glu_A3_dilution100*glu_A3_mean_conc100), (glu_A3_dilution100*glu_A3_mean_conc100*homogenate_volume_uL)/wt_A3, + glu_A4_dilution100, glu_A4_mean_lum100, glu_A4_mean_conc100, (glu_A4_dilution100*glu_A4_mean_conc100), (glu_A4_dilution100*glu_A4_mean_conc100*homogenate_volume_uL)/wt_A4, + glu_A5_dilution100, glu_A5_mean_lum100, glu_A5_mean_conc100, (glu_A5_dilution100*glu_A5_mean_conc100), (glu_A5_dilution100*glu_A5_mean_conc100*homogenate_volume_uL)/wt_A5), ncol=5, byrow=TRUE) +colnames(tab) <- c('Dilution factor','Luminescence','Calculated glucose (ug/uL)', 'Total glucose (ug/uL)', 'Normalized glucose (ug/mg tissue)') rownames(tab) <- c('A1.df20','A2.df20','A3.df20','A4.df20','A5.df20','A1.df100','A2.df100','A3.df100','A4.df100','Af.df100' ) tab <- as.table(tab) tab diff --git a/Glycogen/code/Gen5-20260204-mgig-glycogenglo.Rmd b/Glycogen/code/Gen5-20260204-mgig-glycogenglo.Rmd index b977bd1..6ce4fec 100644 --- a/Glycogen/code/Gen5-20260204-mgig-glycogenglo.Rmd +++ b/Glycogen/code/Gen5-20260204-mgig-glycogenglo.Rmd @@ -26,6 +26,16 @@ knitr::opts_chunk$set( plate_layout <- read.csv("https://raw.githubusercontent.com/RobertsLab/sormi-assay-development/refs/heads/main/Glycogen/data/raw_luminescence/layout-Gen5-20260204-mgig-glycogenglo.csv", header = FALSE) raw_luminescence <- read.csv("https://raw.githubusercontent.com/RobertsLab/sormi-assay-development/refs/heads/main/Glycogen/data/raw_luminescence/raw_lum-Gen5-20260204-mgig-glycogenglo.csv", header = FALSE) +tissue_weights <- read.csv("https://raw.githubusercontent.com/RobertsLab/sormi-assay-development/refs/heads/main/Glycogen/data/20251210-mgig-ctenidia_weights-glycogen_assay.csv") + +# Homogenate volume (µL): 750 µL PBS/HCl + 250 µL TRIS buffer = 1000 µL total +homogenate_volume_uL <- 1000 + +# Helper function to extract tissue weight from plate layout label +# Label format: "---df.", e.g., "A6-glyc-25-df.20" +get_weight_from_label <- function(label) { + as.numeric(gsub("^[^-]+-[a-z]+-([0-9.]+)-df.*", "\\1", as.character(label))) +} cat("Plate layout:\n") str(plate_layout) @@ -577,17 +587,28 @@ for (i in 1:nrow(glycogen_summary_data)) { ```{r, sample glycogen calculations} -tab <- matrix(c(glyc_A6_dilution, glyc_A6_mean_lum, glyc_A6_mean_conc, (glyc_A6_dilution*glyc_A6_mean_conc), - glyc_A7_dilution, glyc_A7_mean_lum, glyc_A7_mean_conc, (glyc_A7_dilution*glyc_A7_mean_conc), - glyc_A8_dilution, glyc_A8_mean_lum, glyc_A8_mean_conc, (glyc_A8_dilution*glyc_A8_mean_conc), - glyc_B1_dilution, glyc_B1_mean_lum, glyc_B1_mean_conc, (glyc_B1_dilution*glyc_B1_mean_conc), - glyc_B2_dilution, glyc_B2_mean_lum, glyc_B2_mean_conc, (glyc_B2_dilution*glyc_B2_mean_conc), - glyc_B3_dilution, glyc_B3_mean_lum, glyc_B3_mean_conc, (glyc_B3_dilution*glyc_B3_mean_conc), - glyc_B4_dilution, glyc_B4_mean_lum, glyc_B4_mean_conc, (glyc_B4_dilution*glyc_B4_mean_conc), - glyc_B5_dilution, glyc_B5_mean_lum, glyc_B5_mean_conc, (glyc_B5_dilution*glyc_B5_mean_conc), - glyc_B6_dilution, glyc_B6_mean_lum, glyc_B6_mean_conc, (glyc_B6_dilution*glyc_B6_mean_conc), - glyc_B7_dilution, glyc_B7_mean_lum, glyc_B7_mean_conc, (glyc_B7_dilution*glyc_B7_mean_conc)), ncol=4, byrow=TRUE) -colnames(tab) <- c('Dilution factor','Luminescence','Calculated Glycogen (ug/uL)', 'Total glycogen (ug/uL)') +wt_A6 <- get_weight_from_label(plate_layout[1, 1]) +wt_A7 <- get_weight_from_label(plate_layout[2, 1]) +wt_A8 <- get_weight_from_label(plate_layout[3, 1]) +wt_B1 <- get_weight_from_label(plate_layout[4, 1]) +wt_B2 <- get_weight_from_label(plate_layout[5, 1]) +wt_B3 <- get_weight_from_label(plate_layout[1, 4]) +wt_B4 <- get_weight_from_label(plate_layout[2, 4]) +wt_B5 <- get_weight_from_label(plate_layout[3, 4]) +wt_B6 <- get_weight_from_label(plate_layout[4, 4]) +wt_B7 <- get_weight_from_label(plate_layout[5, 4]) + +tab <- matrix(c(glyc_A6_dilution, glyc_A6_mean_lum, glyc_A6_mean_conc, (glyc_A6_dilution*glyc_A6_mean_conc), (glyc_A6_dilution*glyc_A6_mean_conc*homogenate_volume_uL)/wt_A6, + glyc_A7_dilution, glyc_A7_mean_lum, glyc_A7_mean_conc, (glyc_A7_dilution*glyc_A7_mean_conc), (glyc_A7_dilution*glyc_A7_mean_conc*homogenate_volume_uL)/wt_A7, + glyc_A8_dilution, glyc_A8_mean_lum, glyc_A8_mean_conc, (glyc_A8_dilution*glyc_A8_mean_conc), (glyc_A8_dilution*glyc_A8_mean_conc*homogenate_volume_uL)/wt_A8, + glyc_B1_dilution, glyc_B1_mean_lum, glyc_B1_mean_conc, (glyc_B1_dilution*glyc_B1_mean_conc), (glyc_B1_dilution*glyc_B1_mean_conc*homogenate_volume_uL)/wt_B1, + glyc_B2_dilution, glyc_B2_mean_lum, glyc_B2_mean_conc, (glyc_B2_dilution*glyc_B2_mean_conc), (glyc_B2_dilution*glyc_B2_mean_conc*homogenate_volume_uL)/wt_B2, + glyc_B3_dilution, glyc_B3_mean_lum, glyc_B3_mean_conc, (glyc_B3_dilution*glyc_B3_mean_conc), (glyc_B3_dilution*glyc_B3_mean_conc*homogenate_volume_uL)/wt_B3, + glyc_B4_dilution, glyc_B4_mean_lum, glyc_B4_mean_conc, (glyc_B4_dilution*glyc_B4_mean_conc), (glyc_B4_dilution*glyc_B4_mean_conc*homogenate_volume_uL)/wt_B4, + glyc_B5_dilution, glyc_B5_mean_lum, glyc_B5_mean_conc, (glyc_B5_dilution*glyc_B5_mean_conc), (glyc_B5_dilution*glyc_B5_mean_conc*homogenate_volume_uL)/wt_B5, + glyc_B6_dilution, glyc_B6_mean_lum, glyc_B6_mean_conc, (glyc_B6_dilution*glyc_B6_mean_conc), (glyc_B6_dilution*glyc_B6_mean_conc*homogenate_volume_uL)/wt_B6, + glyc_B7_dilution, glyc_B7_mean_lum, glyc_B7_mean_conc, (glyc_B7_dilution*glyc_B7_mean_conc), (glyc_B7_dilution*glyc_B7_mean_conc*homogenate_volume_uL)/wt_B7), ncol=5, byrow=TRUE) +colnames(tab) <- c('Dilution factor','Luminescence','Calculated Glycogen (ug/uL)', 'Total glycogen (ug/uL)', 'Normalized glycogen (ug/mg tissue)') rownames(tab) <- c('A6','A7','A8','B1','B2','B3','B4','B5','B6','B7' ) tab <- as.table(tab) tab @@ -1132,17 +1153,17 @@ for (i in 1:nrow(glucose_summary_data)) { ```{r, sample glucose calculations} -tab <- matrix(c(glu_A6_dilution, glu_A6_mean_lum, glu_A6_mean_conc, (glu_A6_dilution*glu_A6_mean_conc), - glu_A7_dilution, glu_A7_mean_lum, glu_A7_mean_conc, (glu_A7_dilution*glu_A7_mean_conc), - glu_A8_dilution, glu_A8_mean_lum, glu_A8_mean_conc, (glu_A8_dilution*glu_A8_mean_conc), - glu_B1_dilution, glu_B1_mean_lum, glu_B1_mean_conc, (glu_B1_dilution*glu_B1_mean_conc), - glu_B2_dilution, glu_B2_mean_lum, glu_B2_mean_conc, (glu_B2_dilution*glu_B2_mean_conc), - glu_B3_dilution, glu_B3_mean_lum, glu_B3_mean_conc, (glu_B3_dilution*glu_B3_mean_conc), - glu_B4_dilution, glu_B4_mean_lum, glu_B4_mean_conc, (glu_B4_dilution*glu_B4_mean_conc), - glu_B5_dilution, glu_B5_mean_lum, glu_B5_mean_conc, (glu_B5_dilution*glu_B5_mean_conc), - glu_B6_dilution, glu_B6_mean_lum, glu_B6_mean_conc, (glu_B6_dilution*glu_B6_mean_conc), - glu_B7_dilution, glu_B7_mean_lum, glu_B7_mean_conc, (glu_B7_dilution*glu_B7_mean_conc)), ncol=4, byrow=TRUE) -colnames(tab) <- c('Dilution factor','Luminescence','Calculated glucose (ug/uL)', 'Total glucose (ug/uL)') +tab <- matrix(c(glu_A6_dilution, glu_A6_mean_lum, glu_A6_mean_conc, (glu_A6_dilution*glu_A6_mean_conc), (glu_A6_dilution*glu_A6_mean_conc*homogenate_volume_uL)/wt_A6, + glu_A7_dilution, glu_A7_mean_lum, glu_A7_mean_conc, (glu_A7_dilution*glu_A7_mean_conc), (glu_A7_dilution*glu_A7_mean_conc*homogenate_volume_uL)/wt_A7, + glu_A8_dilution, glu_A8_mean_lum, glu_A8_mean_conc, (glu_A8_dilution*glu_A8_mean_conc), (glu_A8_dilution*glu_A8_mean_conc*homogenate_volume_uL)/wt_A8, + glu_B1_dilution, glu_B1_mean_lum, glu_B1_mean_conc, (glu_B1_dilution*glu_B1_mean_conc), (glu_B1_dilution*glu_B1_mean_conc*homogenate_volume_uL)/wt_B1, + glu_B2_dilution, glu_B2_mean_lum, glu_B2_mean_conc, (glu_B2_dilution*glu_B2_mean_conc), (glu_B2_dilution*glu_B2_mean_conc*homogenate_volume_uL)/wt_B2, + glu_B3_dilution, glu_B3_mean_lum, glu_B3_mean_conc, (glu_B3_dilution*glu_B3_mean_conc), (glu_B3_dilution*glu_B3_mean_conc*homogenate_volume_uL)/wt_B3, + glu_B4_dilution, glu_B4_mean_lum, glu_B4_mean_conc, (glu_B4_dilution*glu_B4_mean_conc), (glu_B4_dilution*glu_B4_mean_conc*homogenate_volume_uL)/wt_B4, + glu_B5_dilution, glu_B5_mean_lum, glu_B5_mean_conc, (glu_B5_dilution*glu_B5_mean_conc), (glu_B5_dilution*glu_B5_mean_conc*homogenate_volume_uL)/wt_B5, + glu_B6_dilution, glu_B6_mean_lum, glu_B6_mean_conc, (glu_B6_dilution*glu_B6_mean_conc), (glu_B6_dilution*glu_B6_mean_conc*homogenate_volume_uL)/wt_B6, + glu_B7_dilution, glu_B7_mean_lum, glu_B7_mean_conc, (glu_B7_dilution*glu_B7_mean_conc), (glu_B7_dilution*glu_B7_mean_conc*homogenate_volume_uL)/wt_B7), ncol=5, byrow=TRUE) +colnames(tab) <- c('Dilution factor','Luminescence','Calculated glucose (ug/uL)', 'Total glucose (ug/uL)', 'Normalized glucose (ug/mg tissue)') rownames(tab) <- c('A6','A7','A8','B1','B2','B3','B4','B5','B6','B7' ) tab <- as.table(tab) tab diff --git a/Glycogen/code/Gen5-20260206-mgig-glycogenglo.Rmd b/Glycogen/code/Gen5-20260206-mgig-glycogenglo.Rmd index 915ea7e..f9762be 100644 --- a/Glycogen/code/Gen5-20260206-mgig-glycogenglo.Rmd +++ b/Glycogen/code/Gen5-20260206-mgig-glycogenglo.Rmd @@ -26,6 +26,16 @@ knitr::opts_chunk$set( plate_layout <- read.csv("https://raw.githubusercontent.com/RobertsLab/sormi-assay-development/refs/heads/main/Glycogen/data/raw_luminescence/layout-Gen5-20260206-mgig-glycogenglo.csv", header = FALSE) raw_luminescence <- read.csv("https://raw.githubusercontent.com/RobertsLab/sormi-assay-development/refs/heads/main/Glycogen/data/raw_luminescence/raw_lum-Gen5-20260206-mgig-glycogenglo.csv", header = FALSE) +tissue_weights <- read.csv("https://raw.githubusercontent.com/RobertsLab/sormi-assay-development/refs/heads/main/Glycogen/data/20251210-mgig-ctenidia_weights-glycogen_assay.csv") + +# Homogenate volume (µL): 750 µL PBS/HCl + 250 µL TRIS buffer = 1000 µL total +homogenate_volume_uL <- 1000 + +# Helper function to extract tissue weight from plate layout label +# Label format: "---df.", e.g., "B8-glyc-31-df.20" +get_weight_from_label <- function(label) { + as.numeric(gsub("^[^-]+-[a-z]+-([0-9.]+)-df.*", "\\1", as.character(label))) +} cat("Plate layout:\n") str(plate_layout) @@ -584,17 +594,28 @@ for (i in 1:nrow(glycogen_summary_data)) { ```{r, sample glycogen calculations} -tab <- matrix(c(glyc_B8_dilution, glyc_B8_mean_lum, glyc_B8_mean_conc, (glyc_B8_dilution*glyc_B8_mean_conc), - glyc_C1_dilution, glyc_C1_mean_lum, glyc_C1_mean_conc, (glyc_C1_dilution*glyc_C1_mean_conc), - glyc_C2_dilution, glyc_C2_mean_lum, glyc_C2_mean_conc, (glyc_C2_dilution*glyc_C2_mean_conc), - glyc_C3_dilution, glyc_C3_mean_lum, glyc_C3_mean_conc, (glyc_C3_dilution*glyc_C3_mean_conc), - glyc_C4_dilution, glyc_C4_mean_lum, glyc_C4_mean_conc, (glyc_C4_dilution*glyc_C4_mean_conc), - glyc_C5_dilution, glyc_C5_mean_lum, glyc_C5_mean_conc, (glyc_C5_dilution*glyc_C5_mean_conc), - glyc_C6_dilution, glyc_C6_mean_lum, glyc_C6_mean_conc, (glyc_C6_dilution*glyc_C6_mean_conc), - glyc_C7_dilution, glyc_C7_mean_lum, glyc_C7_mean_conc, (glyc_C7_dilution*glyc_C7_mean_conc), - glyc_C8_dilution, glyc_C8_mean_lum, glyc_C8_mean_conc, (glyc_C8_dilution*glyc_C8_mean_conc), - glyc_D1_dilution, glyc_D1_mean_lum, glyc_D1_mean_conc, (glyc_D1_dilution*glyc_D1_mean_conc)), ncol=4, byrow=TRUE) -colnames(tab) <- c('Dilution factor','Luminescence','Calculated Glycogen (ug/uL)', 'Total glycogen (ug/uL)') +wt_B8 <- get_weight_from_label(plate_layout[1, 1]) +wt_C1 <- get_weight_from_label(plate_layout[2, 1]) +wt_C2 <- get_weight_from_label(plate_layout[3, 1]) +wt_C3 <- get_weight_from_label(plate_layout[4, 1]) +wt_C4 <- get_weight_from_label(plate_layout[5, 1]) +wt_C5 <- get_weight_from_label(plate_layout[1, 4]) +wt_C6 <- get_weight_from_label(plate_layout[2, 4]) +wt_C7 <- get_weight_from_label(plate_layout[3, 4]) +wt_C8 <- get_weight_from_label(plate_layout[4, 4]) +wt_D1 <- get_weight_from_label(plate_layout[5, 4]) + +tab <- matrix(c(glyc_B8_dilution, glyc_B8_mean_lum, glyc_B8_mean_conc, (glyc_B8_dilution*glyc_B8_mean_conc), (glyc_B8_dilution*glyc_B8_mean_conc*homogenate_volume_uL)/wt_B8, + glyc_C1_dilution, glyc_C1_mean_lum, glyc_C1_mean_conc, (glyc_C1_dilution*glyc_C1_mean_conc), (glyc_C1_dilution*glyc_C1_mean_conc*homogenate_volume_uL)/wt_C1, + glyc_C2_dilution, glyc_C2_mean_lum, glyc_C2_mean_conc, (glyc_C2_dilution*glyc_C2_mean_conc), (glyc_C2_dilution*glyc_C2_mean_conc*homogenate_volume_uL)/wt_C2, + glyc_C3_dilution, glyc_C3_mean_lum, glyc_C3_mean_conc, (glyc_C3_dilution*glyc_C3_mean_conc), (glyc_C3_dilution*glyc_C3_mean_conc*homogenate_volume_uL)/wt_C3, + glyc_C4_dilution, glyc_C4_mean_lum, glyc_C4_mean_conc, (glyc_C4_dilution*glyc_C4_mean_conc), (glyc_C4_dilution*glyc_C4_mean_conc*homogenate_volume_uL)/wt_C4, + glyc_C5_dilution, glyc_C5_mean_lum, glyc_C5_mean_conc, (glyc_C5_dilution*glyc_C5_mean_conc), (glyc_C5_dilution*glyc_C5_mean_conc*homogenate_volume_uL)/wt_C5, + glyc_C6_dilution, glyc_C6_mean_lum, glyc_C6_mean_conc, (glyc_C6_dilution*glyc_C6_mean_conc), (glyc_C6_dilution*glyc_C6_mean_conc*homogenate_volume_uL)/wt_C6, + glyc_C7_dilution, glyc_C7_mean_lum, glyc_C7_mean_conc, (glyc_C7_dilution*glyc_C7_mean_conc), (glyc_C7_dilution*glyc_C7_mean_conc*homogenate_volume_uL)/wt_C7, + glyc_C8_dilution, glyc_C8_mean_lum, glyc_C8_mean_conc, (glyc_C8_dilution*glyc_C8_mean_conc), (glyc_C8_dilution*glyc_C8_mean_conc*homogenate_volume_uL)/wt_C8, + glyc_D1_dilution, glyc_D1_mean_lum, glyc_D1_mean_conc, (glyc_D1_dilution*glyc_D1_mean_conc), (glyc_D1_dilution*glyc_D1_mean_conc*homogenate_volume_uL)/wt_D1), ncol=5, byrow=TRUE) +colnames(tab) <- c('Dilution factor','Luminescence','Calculated Glycogen (ug/uL)', 'Total glycogen (ug/uL)', 'Normalized glycogen (ug/mg tissue)') rownames(tab) <- c('B8','C1','C2','C3','C4','C5','C6','C7','C8','D1' ) tab <- as.table(tab) tab @@ -1140,17 +1161,17 @@ for (i in 1:nrow(glucose_summary_data)) { ```{r, sample glucose calculations} -tab <- matrix(c(glu_B8_dilution, glu_B8_mean_lum, glu_B8_mean_conc, (glu_B8_dilution*glu_B8_mean_conc), - glu_C1_dilution, glu_C1_mean_lum, glu_C1_mean_conc, (glu_C1_dilution*glu_C1_mean_conc), - glu_C2_dilution, glu_C2_mean_lum, glu_C2_mean_conc, (glu_C2_dilution*glu_C2_mean_conc), - glu_C3_dilution, glu_C3_mean_lum, glu_C3_mean_conc, (glu_C3_dilution*glu_C3_mean_conc), - glu_C4_dilution, glu_C4_mean_lum, glu_C4_mean_conc, (glu_C4_dilution*glu_C4_mean_conc), - glu_C5_dilution, glu_C5_mean_lum, glu_C5_mean_conc, (glu_C5_dilution*glu_C5_mean_conc), - glu_C6_dilution, glu_C6_mean_lum, glu_C6_mean_conc, (glu_C6_dilution*glu_C6_mean_conc), - glu_C7_dilution, glu_C7_mean_lum, glu_C7_mean_conc, (glu_C7_dilution*glu_C7_mean_conc), - glu_C8_dilution, glu_C8_mean_lum, glu_C8_mean_conc, (glu_C8_dilution*glu_C8_mean_conc), - glu_D1_dilution, glu_D1_mean_lum, glu_D1_mean_conc, (glu_D1_dilution*glu_D1_mean_conc)), ncol=4, byrow=TRUE) -colnames(tab) <- c('Dilution factor','Luminescence','Calculated glucose (ug/uL)', 'Total glucose (ug/uL)') +tab <- matrix(c(glu_B8_dilution, glu_B8_mean_lum, glu_B8_mean_conc, (glu_B8_dilution*glu_B8_mean_conc), (glu_B8_dilution*glu_B8_mean_conc*homogenate_volume_uL)/wt_B8, + glu_C1_dilution, glu_C1_mean_lum, glu_C1_mean_conc, (glu_C1_dilution*glu_C1_mean_conc), (glu_C1_dilution*glu_C1_mean_conc*homogenate_volume_uL)/wt_C1, + glu_C2_dilution, glu_C2_mean_lum, glu_C2_mean_conc, (glu_C2_dilution*glu_C2_mean_conc), (glu_C2_dilution*glu_C2_mean_conc*homogenate_volume_uL)/wt_C2, + glu_C3_dilution, glu_C3_mean_lum, glu_C3_mean_conc, (glu_C3_dilution*glu_C3_mean_conc), (glu_C3_dilution*glu_C3_mean_conc*homogenate_volume_uL)/wt_C3, + glu_C4_dilution, glu_C4_mean_lum, glu_C4_mean_conc, (glu_C4_dilution*glu_C4_mean_conc), (glu_C4_dilution*glu_C4_mean_conc*homogenate_volume_uL)/wt_C4, + glu_C5_dilution, glu_C5_mean_lum, glu_C5_mean_conc, (glu_C5_dilution*glu_C5_mean_conc), (glu_C5_dilution*glu_C5_mean_conc*homogenate_volume_uL)/wt_C5, + glu_C6_dilution, glu_C6_mean_lum, glu_C6_mean_conc, (glu_C6_dilution*glu_C6_mean_conc), (glu_C6_dilution*glu_C6_mean_conc*homogenate_volume_uL)/wt_C6, + glu_C7_dilution, glu_C7_mean_lum, glu_C7_mean_conc, (glu_C7_dilution*glu_C7_mean_conc), (glu_C7_dilution*glu_C7_mean_conc*homogenate_volume_uL)/wt_C7, + glu_C8_dilution, glu_C8_mean_lum, glu_C8_mean_conc, (glu_C8_dilution*glu_C8_mean_conc), (glu_C8_dilution*glu_C8_mean_conc*homogenate_volume_uL)/wt_C8, + glu_D1_dilution, glu_D1_mean_lum, glu_D1_mean_conc, (glu_D1_dilution*glu_D1_mean_conc), (glu_D1_dilution*glu_D1_mean_conc*homogenate_volume_uL)/wt_D1), ncol=5, byrow=TRUE) +colnames(tab) <- c('Dilution factor','Luminescence','Calculated glucose (ug/uL)', 'Total glucose (ug/uL)', 'Normalized glucose (ug/mg tissue)') rownames(tab) <- c('B8','C1','C2','C3','C4','C5','C6','C7','C8','D1' ) tab <- as.table(tab) tab diff --git a/Glycogen/code/Gen5-20260209-mgig-glycogenglo.Rmd b/Glycogen/code/Gen5-20260209-mgig-glycogenglo.Rmd index 4f5e22b..27eadfe 100644 --- a/Glycogen/code/Gen5-20260209-mgig-glycogenglo.Rmd +++ b/Glycogen/code/Gen5-20260209-mgig-glycogenglo.Rmd @@ -26,6 +26,16 @@ knitr::opts_chunk$set( plate_layout <- read.csv("https://raw.githubusercontent.com/RobertsLab/sormi-assay-development/refs/heads/main/Glycogen/data/raw_luminescence/layout-Gen5-20260209-mgig-glycogenglo.csv", header = FALSE) raw_luminescence <- read.csv("https://raw.githubusercontent.com/RobertsLab/sormi-assay-development/refs/heads/main/Glycogen/data/raw_luminescence/raw_lum-Gen5-20260209-mgig-glycogenglo.csv", header = FALSE) +tissue_weights <- read.csv("https://raw.githubusercontent.com/RobertsLab/sormi-assay-development/refs/heads/main/Glycogen/data/20251210-mgig-ctenidia_weights-glycogen_assay.csv") + +# Homogenate volume (µL): 750 µL PBS/HCl + 250 µL TRIS buffer = 1000 µL total +homogenate_volume_uL <- 1000 + +# Helper function to extract tissue weight from plate layout label +# Label format: "---df.", e.g., "B8-glyc-31-df.20" +get_weight_from_label <- function(label) { + as.numeric(gsub("^[^-]+-[a-z]+-([0-9.]+)-df.*", "\\1", as.character(label))) +} cat("Plate layout:\n") str(plate_layout) @@ -584,17 +594,28 @@ for (i in 1:nrow(glycogen_summary_data)) { ```{r, sample glycogen calculations} -tab <- matrix(c(glyc_B8_dilution, glyc_B8_mean_lum, glyc_B8_mean_conc, (glyc_B8_dilution*glyc_B8_mean_conc), - glyc_C1_dilution, glyc_C1_mean_lum, glyc_C1_mean_conc, (glyc_C1_dilution*glyc_C1_mean_conc), - glyc_C2_dilution, glyc_C2_mean_lum, glyc_C2_mean_conc, (glyc_C2_dilution*glyc_C2_mean_conc), - glyc_C3_dilution, glyc_C3_mean_lum, glyc_C3_mean_conc, (glyc_C3_dilution*glyc_C3_mean_conc), - glyc_C4_dilution, glyc_C4_mean_lum, glyc_C4_mean_conc, (glyc_C4_dilution*glyc_C4_mean_conc), - glyc_C5_dilution, glyc_C5_mean_lum, glyc_C5_mean_conc, (glyc_C5_dilution*glyc_C5_mean_conc), - glyc_C6_dilution, glyc_C6_mean_lum, glyc_C6_mean_conc, (glyc_C6_dilution*glyc_C6_mean_conc), - glyc_C7_dilution, glyc_C7_mean_lum, glyc_C7_mean_conc, (glyc_C7_dilution*glyc_C7_mean_conc), - glyc_C8_dilution, glyc_C8_mean_lum, glyc_C8_mean_conc, (glyc_C8_dilution*glyc_C8_mean_conc), - glyc_D1_dilution, glyc_D1_mean_lum, glyc_D1_mean_conc, (glyc_D1_dilution*glyc_D1_mean_conc)), ncol=4, byrow=TRUE) -colnames(tab) <- c('Dilution factor','Luminescence','Calculated Glycogen (ug/uL)', 'Total glycogen (ug/uL)') +wt_B8 <- get_weight_from_label(plate_layout[1, 1]) +wt_C1 <- get_weight_from_label(plate_layout[2, 1]) +wt_C2 <- get_weight_from_label(plate_layout[3, 1]) +wt_C3 <- get_weight_from_label(plate_layout[4, 1]) +wt_C4 <- get_weight_from_label(plate_layout[5, 1]) +wt_C5 <- get_weight_from_label(plate_layout[1, 4]) +wt_C6 <- get_weight_from_label(plate_layout[2, 4]) +wt_C7 <- get_weight_from_label(plate_layout[3, 4]) +wt_C8 <- get_weight_from_label(plate_layout[4, 4]) +wt_D1 <- get_weight_from_label(plate_layout[5, 4]) + +tab <- matrix(c(glyc_B8_dilution, glyc_B8_mean_lum, glyc_B8_mean_conc, (glyc_B8_dilution*glyc_B8_mean_conc), (glyc_B8_dilution*glyc_B8_mean_conc*homogenate_volume_uL)/wt_B8, + glyc_C1_dilution, glyc_C1_mean_lum, glyc_C1_mean_conc, (glyc_C1_dilution*glyc_C1_mean_conc), (glyc_C1_dilution*glyc_C1_mean_conc*homogenate_volume_uL)/wt_C1, + glyc_C2_dilution, glyc_C2_mean_lum, glyc_C2_mean_conc, (glyc_C2_dilution*glyc_C2_mean_conc), (glyc_C2_dilution*glyc_C2_mean_conc*homogenate_volume_uL)/wt_C2, + glyc_C3_dilution, glyc_C3_mean_lum, glyc_C3_mean_conc, (glyc_C3_dilution*glyc_C3_mean_conc), (glyc_C3_dilution*glyc_C3_mean_conc*homogenate_volume_uL)/wt_C3, + glyc_C4_dilution, glyc_C4_mean_lum, glyc_C4_mean_conc, (glyc_C4_dilution*glyc_C4_mean_conc), (glyc_C4_dilution*glyc_C4_mean_conc*homogenate_volume_uL)/wt_C4, + glyc_C5_dilution, glyc_C5_mean_lum, glyc_C5_mean_conc, (glyc_C5_dilution*glyc_C5_mean_conc), (glyc_C5_dilution*glyc_C5_mean_conc*homogenate_volume_uL)/wt_C5, + glyc_C6_dilution, glyc_C6_mean_lum, glyc_C6_mean_conc, (glyc_C6_dilution*glyc_C6_mean_conc), (glyc_C6_dilution*glyc_C6_mean_conc*homogenate_volume_uL)/wt_C6, + glyc_C7_dilution, glyc_C7_mean_lum, glyc_C7_mean_conc, (glyc_C7_dilution*glyc_C7_mean_conc), (glyc_C7_dilution*glyc_C7_mean_conc*homogenate_volume_uL)/wt_C7, + glyc_C8_dilution, glyc_C8_mean_lum, glyc_C8_mean_conc, (glyc_C8_dilution*glyc_C8_mean_conc), (glyc_C8_dilution*glyc_C8_mean_conc*homogenate_volume_uL)/wt_C8, + glyc_D1_dilution, glyc_D1_mean_lum, glyc_D1_mean_conc, (glyc_D1_dilution*glyc_D1_mean_conc), (glyc_D1_dilution*glyc_D1_mean_conc*homogenate_volume_uL)/wt_D1), ncol=5, byrow=TRUE) +colnames(tab) <- c('Dilution factor','Luminescence','Calculated Glycogen (ug/uL)', 'Total glycogen (ug/uL)', 'Normalized glycogen (ug/mg tissue)') rownames(tab) <- c('B8','C1','C2','C3','C4','C5','C6','C7','C8','D1' ) tab <- as.table(tab) tab @@ -1140,17 +1161,17 @@ for (i in 1:nrow(glucose_summary_data)) { ```{r, sample glucose calculations} -tab <- matrix(c(glu_B8_dilution, glu_B8_mean_lum, glu_B8_mean_conc, (glu_B8_dilution*glu_B8_mean_conc), - glu_C1_dilution, glu_C1_mean_lum, glu_C1_mean_conc, (glu_C1_dilution*glu_C1_mean_conc), - glu_C2_dilution, glu_C2_mean_lum, glu_C2_mean_conc, (glu_C2_dilution*glu_C2_mean_conc), - glu_C3_dilution, glu_C3_mean_lum, glu_C3_mean_conc, (glu_C3_dilution*glu_C3_mean_conc), - glu_C4_dilution, glu_C4_mean_lum, glu_C4_mean_conc, (glu_C4_dilution*glu_C4_mean_conc), - glu_C5_dilution, glu_C5_mean_lum, glu_C5_mean_conc, (glu_C5_dilution*glu_C5_mean_conc), - glu_C6_dilution, glu_C6_mean_lum, glu_C6_mean_conc, (glu_C6_dilution*glu_C6_mean_conc), - glu_C7_dilution, glu_C7_mean_lum, glu_C7_mean_conc, (glu_C7_dilution*glu_C7_mean_conc), - glu_C8_dilution, glu_C8_mean_lum, glu_C8_mean_conc, (glu_C8_dilution*glu_C8_mean_conc), - glu_D1_dilution, glu_D1_mean_lum, glu_D1_mean_conc, (glu_D1_dilution*glu_D1_mean_conc)), ncol=4, byrow=TRUE) -colnames(tab) <- c('Dilution factor','Luminescence','Calculated glucose (ug/uL)', 'Total glucose (ug/uL)') +tab <- matrix(c(glu_B8_dilution, glu_B8_mean_lum, glu_B8_mean_conc, (glu_B8_dilution*glu_B8_mean_conc), (glu_B8_dilution*glu_B8_mean_conc*homogenate_volume_uL)/wt_B8, + glu_C1_dilution, glu_C1_mean_lum, glu_C1_mean_conc, (glu_C1_dilution*glu_C1_mean_conc), (glu_C1_dilution*glu_C1_mean_conc*homogenate_volume_uL)/wt_C1, + glu_C2_dilution, glu_C2_mean_lum, glu_C2_mean_conc, (glu_C2_dilution*glu_C2_mean_conc), (glu_C2_dilution*glu_C2_mean_conc*homogenate_volume_uL)/wt_C2, + glu_C3_dilution, glu_C3_mean_lum, glu_C3_mean_conc, (glu_C3_dilution*glu_C3_mean_conc), (glu_C3_dilution*glu_C3_mean_conc*homogenate_volume_uL)/wt_C3, + glu_C4_dilution, glu_C4_mean_lum, glu_C4_mean_conc, (glu_C4_dilution*glu_C4_mean_conc), (glu_C4_dilution*glu_C4_mean_conc*homogenate_volume_uL)/wt_C4, + glu_C5_dilution, glu_C5_mean_lum, glu_C5_mean_conc, (glu_C5_dilution*glu_C5_mean_conc), (glu_C5_dilution*glu_C5_mean_conc*homogenate_volume_uL)/wt_C5, + glu_C6_dilution, glu_C6_mean_lum, glu_C6_mean_conc, (glu_C6_dilution*glu_C6_mean_conc), (glu_C6_dilution*glu_C6_mean_conc*homogenate_volume_uL)/wt_C6, + glu_C7_dilution, glu_C7_mean_lum, glu_C7_mean_conc, (glu_C7_dilution*glu_C7_mean_conc), (glu_C7_dilution*glu_C7_mean_conc*homogenate_volume_uL)/wt_C7, + glu_C8_dilution, glu_C8_mean_lum, glu_C8_mean_conc, (glu_C8_dilution*glu_C8_mean_conc), (glu_C8_dilution*glu_C8_mean_conc*homogenate_volume_uL)/wt_C8, + glu_D1_dilution, glu_D1_mean_lum, glu_D1_mean_conc, (glu_D1_dilution*glu_D1_mean_conc), (glu_D1_dilution*glu_D1_mean_conc*homogenate_volume_uL)/wt_D1), ncol=5, byrow=TRUE) +colnames(tab) <- c('Dilution factor','Luminescence','Calculated glucose (ug/uL)', 'Total glucose (ug/uL)', 'Normalized glucose (ug/mg tissue)') rownames(tab) <- c('B8','C1','C2','C3','C4','C5','C6','C7','C8','D1' ) tab <- as.table(tab) tab diff --git a/Glycogen/code/Gen5-20260213-mgig-glycogenglo.Rmd b/Glycogen/code/Gen5-20260213-mgig-glycogenglo.Rmd index 4b503fc..4d7f2f6 100644 --- a/Glycogen/code/Gen5-20260213-mgig-glycogenglo.Rmd +++ b/Glycogen/code/Gen5-20260213-mgig-glycogenglo.Rmd @@ -26,6 +26,16 @@ knitr::opts_chunk$set( plate_layout <- read.csv("https://raw.githubusercontent.com/RobertsLab/sormi-assay-development/refs/heads/main/Glycogen/data/raw_luminescence/layout-Gen5-20260213-mgig-glycogenglo.csv", header = FALSE) raw_luminescence <- read.csv("https://raw.githubusercontent.com/RobertsLab/sormi-assay-development/refs/heads/main/Glycogen/data/raw_luminescence/raw_lum-Gen5-20260213-mgig-glycogenglo.csv", header = FALSE) +tissue_weights <- read.csv("https://raw.githubusercontent.com/RobertsLab/sormi-assay-development/refs/heads/main/Glycogen/data/20251210-mgig-ctenidia_weights-glycogen_assay.csv") + +# Homogenate volume (µL): 750 µL PBS/HCl + 250 µL TRIS buffer = 1000 µL total +homogenate_volume_uL <- 1000 + +# Helper function to extract tissue weight from plate layout label +# Label format: "---df.", e.g., "D2-glyc-22-df.20" +get_weight_from_label <- function(label) { + as.numeric(gsub("^[^-]+-[a-z]+-([0-9.]+)-df.*", "\\1", as.character(label))) +} cat("Plate layout:\n") str(plate_layout) @@ -584,17 +594,28 @@ for (i in 1:nrow(glycogen_summary_data)) { ```{r, sample glycogen calculations} -tab <- matrix(c(glyc_D2_dilution, glyc_D2_mean_lum, glyc_D2_mean_conc, (glyc_D2_dilution*glyc_D2_mean_conc), - glyc_D3_dilution, glyc_D3_mean_lum, glyc_D3_mean_conc, (glyc_D3_dilution*glyc_D3_mean_conc), - glyc_D4_dilution, glyc_D4_mean_lum, glyc_D4_mean_conc, (glyc_D4_dilution*glyc_D4_mean_conc), - glyc_D5_dilution, glyc_D5_mean_lum, glyc_D5_mean_conc, (glyc_D5_dilution*glyc_D5_mean_conc), - glyc_D6_dilution, glyc_D6_mean_lum, glyc_D6_mean_conc, (glyc_D6_dilution*glyc_D6_mean_conc), - glyc_D7_dilution, glyc_D7_mean_lum, glyc_D7_mean_conc, (glyc_D7_dilution*glyc_D7_mean_conc), - glyc_D8_dilution, glyc_D8_mean_lum, glyc_D8_mean_conc, (glyc_D8_dilution*glyc_D8_mean_conc), - glyc_E1_dilution, glyc_E1_mean_lum, glyc_E1_mean_conc, (glyc_E1_dilution*glyc_E1_mean_conc), - glyc_E2_dilution, glyc_E2_mean_lum, glyc_E2_mean_conc, (glyc_E2_dilution*glyc_E2_mean_conc), - glyc_E3_dilution, glyc_E3_mean_lum, glyc_E3_mean_conc, (glyc_E3_dilution*glyc_E3_mean_conc)), ncol=4, byrow=TRUE) -colnames(tab) <- c('Dilution factor','Luminescence','Calculated Glycogen (ug/uL)', 'Total glycogen (ug/uL)') +wt_D2 <- get_weight_from_label(plate_layout[1, 1]) +wt_D3 <- get_weight_from_label(plate_layout[2, 1]) +wt_D4 <- get_weight_from_label(plate_layout[3, 1]) +wt_D5 <- get_weight_from_label(plate_layout[4, 1]) +wt_D6 <- get_weight_from_label(plate_layout[5, 1]) +wt_D7 <- get_weight_from_label(plate_layout[1, 4]) +wt_D8 <- get_weight_from_label(plate_layout[2, 4]) +wt_E1 <- get_weight_from_label(plate_layout[3, 4]) +wt_E2 <- get_weight_from_label(plate_layout[4, 4]) +wt_E3 <- get_weight_from_label(plate_layout[5, 4]) + +tab <- matrix(c(glyc_D2_dilution, glyc_D2_mean_lum, glyc_D2_mean_conc, (glyc_D2_dilution*glyc_D2_mean_conc), (glyc_D2_dilution*glyc_D2_mean_conc*homogenate_volume_uL)/wt_D2, + glyc_D3_dilution, glyc_D3_mean_lum, glyc_D3_mean_conc, (glyc_D3_dilution*glyc_D3_mean_conc), (glyc_D3_dilution*glyc_D3_mean_conc*homogenate_volume_uL)/wt_D3, + glyc_D4_dilution, glyc_D4_mean_lum, glyc_D4_mean_conc, (glyc_D4_dilution*glyc_D4_mean_conc), (glyc_D4_dilution*glyc_D4_mean_conc*homogenate_volume_uL)/wt_D4, + glyc_D5_dilution, glyc_D5_mean_lum, glyc_D5_mean_conc, (glyc_D5_dilution*glyc_D5_mean_conc), (glyc_D5_dilution*glyc_D5_mean_conc*homogenate_volume_uL)/wt_D5, + glyc_D6_dilution, glyc_D6_mean_lum, glyc_D6_mean_conc, (glyc_D6_dilution*glyc_D6_mean_conc), (glyc_D6_dilution*glyc_D6_mean_conc*homogenate_volume_uL)/wt_D6, + glyc_D7_dilution, glyc_D7_mean_lum, glyc_D7_mean_conc, (glyc_D7_dilution*glyc_D7_mean_conc), (glyc_D7_dilution*glyc_D7_mean_conc*homogenate_volume_uL)/wt_D7, + glyc_D8_dilution, glyc_D8_mean_lum, glyc_D8_mean_conc, (glyc_D8_dilution*glyc_D8_mean_conc), (glyc_D8_dilution*glyc_D8_mean_conc*homogenate_volume_uL)/wt_D8, + glyc_E1_dilution, glyc_E1_mean_lum, glyc_E1_mean_conc, (glyc_E1_dilution*glyc_E1_mean_conc), (glyc_E1_dilution*glyc_E1_mean_conc*homogenate_volume_uL)/wt_E1, + glyc_E2_dilution, glyc_E2_mean_lum, glyc_E2_mean_conc, (glyc_E2_dilution*glyc_E2_mean_conc), (glyc_E2_dilution*glyc_E2_mean_conc*homogenate_volume_uL)/wt_E2, + glyc_E3_dilution, glyc_E3_mean_lum, glyc_E3_mean_conc, (glyc_E3_dilution*glyc_E3_mean_conc), (glyc_E3_dilution*glyc_E3_mean_conc*homogenate_volume_uL)/wt_E3), ncol=5, byrow=TRUE) +colnames(tab) <- c('Dilution factor','Luminescence','Calculated Glycogen (ug/uL)', 'Total glycogen (ug/uL)', 'Normalized glycogen (ug/mg tissue)') rownames(tab) <- c('D2','D3','D4','D5','D6','D7','D8','E1','E2','E3' ) tab <- as.table(tab) tab @@ -1141,17 +1162,17 @@ for (i in 1:nrow(glucose_summary_data)) { ```{r, sample glucose calculations} -tab <- matrix(c(glu_D2_dilution, glu_D2_mean_lum, glu_D2_mean_conc, (glu_D2_dilution*glu_D2_mean_conc), - glu_D3_dilution, glu_D3_mean_lum, glu_D3_mean_conc, (glu_D3_dilution*glu_D3_mean_conc), - glu_D4_dilution, glu_D4_mean_lum, glu_D4_mean_conc, (glu_D4_dilution*glu_D4_mean_conc), - glu_D5_dilution, glu_D5_mean_lum, glu_D5_mean_conc, (glu_D5_dilution*glu_D5_mean_conc), - glu_D6_dilution, glu_D6_mean_lum, glu_D6_mean_conc, (glu_D6_dilution*glu_D6_mean_conc), - glu_D7_dilution, glu_D7_mean_lum, glu_D7_mean_conc, (glu_D7_dilution*glu_D7_mean_conc), - glu_D8_dilution, glu_D8_mean_lum, glu_D8_mean_conc, (glu_D8_dilution*glu_D8_mean_conc), - glu_E1_dilution, glu_E1_mean_lum, glu_E1_mean_conc, (glu_E1_dilution*glu_E1_mean_conc), - glu_E2_dilution, glu_E2_mean_lum, glu_E2_mean_conc, (glu_E2_dilution*glu_E2_mean_conc), - glu_E3_dilution, glu_E3_mean_lum, glu_E3_mean_conc, (glu_E3_dilution*glu_E3_mean_conc)), ncol=4, byrow=TRUE) -colnames(tab) <- c('Dilution factor','Luminescence','Calculated glucose (ug/uL)', 'Total glucose (ug/uL)') +tab <- matrix(c(glu_D2_dilution, glu_D2_mean_lum, glu_D2_mean_conc, (glu_D2_dilution*glu_D2_mean_conc), (glu_D2_dilution*glu_D2_mean_conc*homogenate_volume_uL)/wt_D2, + glu_D3_dilution, glu_D3_mean_lum, glu_D3_mean_conc, (glu_D3_dilution*glu_D3_mean_conc), (glu_D3_dilution*glu_D3_mean_conc*homogenate_volume_uL)/wt_D3, + glu_D4_dilution, glu_D4_mean_lum, glu_D4_mean_conc, (glu_D4_dilution*glu_D4_mean_conc), (glu_D4_dilution*glu_D4_mean_conc*homogenate_volume_uL)/wt_D4, + glu_D5_dilution, glu_D5_mean_lum, glu_D5_mean_conc, (glu_D5_dilution*glu_D5_mean_conc), (glu_D5_dilution*glu_D5_mean_conc*homogenate_volume_uL)/wt_D5, + glu_D6_dilution, glu_D6_mean_lum, glu_D6_mean_conc, (glu_D6_dilution*glu_D6_mean_conc), (glu_D6_dilution*glu_D6_mean_conc*homogenate_volume_uL)/wt_D6, + glu_D7_dilution, glu_D7_mean_lum, glu_D7_mean_conc, (glu_D7_dilution*glu_D7_mean_conc), (glu_D7_dilution*glu_D7_mean_conc*homogenate_volume_uL)/wt_D7, + glu_D8_dilution, glu_D8_mean_lum, glu_D8_mean_conc, (glu_D8_dilution*glu_D8_mean_conc), (glu_D8_dilution*glu_D8_mean_conc*homogenate_volume_uL)/wt_D8, + glu_E1_dilution, glu_E1_mean_lum, glu_E1_mean_conc, (glu_E1_dilution*glu_E1_mean_conc), (glu_E1_dilution*glu_E1_mean_conc*homogenate_volume_uL)/wt_E1, + glu_E2_dilution, glu_E2_mean_lum, glu_E2_mean_conc, (glu_E2_dilution*glu_E2_mean_conc), (glu_E2_dilution*glu_E2_mean_conc*homogenate_volume_uL)/wt_E2, + glu_E3_dilution, glu_E3_mean_lum, glu_E3_mean_conc, (glu_E3_dilution*glu_E3_mean_conc), (glu_E3_dilution*glu_E3_mean_conc*homogenate_volume_uL)/wt_E3), ncol=5, byrow=TRUE) +colnames(tab) <- c('Dilution factor','Luminescence','Calculated glucose (ug/uL)', 'Total glucose (ug/uL)', 'Normalized glucose (ug/mg tissue)') rownames(tab) <- c('D2','D3','D4','D5','D6','D7','D8','E1','E2','E3' ) tab <- as.table(tab) tab diff --git a/Glycogen/code/Gen5-20260218-mgig-glycogenglo.Rmd b/Glycogen/code/Gen5-20260218-mgig-glycogenglo.Rmd index a091e63..3c9b0c0 100644 --- a/Glycogen/code/Gen5-20260218-mgig-glycogenglo.Rmd +++ b/Glycogen/code/Gen5-20260218-mgig-glycogenglo.Rmd @@ -26,6 +26,16 @@ knitr::opts_chunk$set( plate_layout <- read.csv("https://raw.githubusercontent.com/RobertsLab/sormi-assay-development/refs/heads/main/Glycogen/data/raw_luminescence/layout-Gen5-20260218-mgig-glycogenglo.csv", header = FALSE) raw_luminescence <- read.csv("https://raw.githubusercontent.com/RobertsLab/sormi-assay-development/refs/heads/main/Glycogen/data/raw_luminescence/raw_lum-Gen5-20260218-mgig-glycogenglo.csv", header = FALSE) +tissue_weights <- read.csv("https://raw.githubusercontent.com/RobertsLab/sormi-assay-development/refs/heads/main/Glycogen/data/20251210-mgig-ctenidia_weights-glycogen_assay.csv") + +# Homogenate volume (µL): 750 µL PBS/HCl + 250 µL TRIS buffer = 1000 µL total +homogenate_volume_uL <- 1000 + +# Helper function to extract tissue weight from plate layout label +# Label format: "---df.", e.g., "C7-glyc-35-df.50" +get_weight_from_label <- function(label) { + as.numeric(gsub("^[^-]+-[a-z]+-([0-9.]+)-df.*", "\\1", as.character(label))) +} cat("Plate layout:\n") str(plate_layout) @@ -450,14 +460,21 @@ for (i in 1:nrow(glycogen_summary_data)) { ``` ```{r, sample glycogen calculations} -tab <- matrix(c(glyc_C7_dilution50, glyc_C7_mean_lum50, glyc_C7_mean_conc50, (glyc_C7_dilution50*glyc_C7_mean_conc50), - glyc_C7_dilution100, glyc_C7_mean_lum100, glyc_C7_mean_conc100, (glyc_C7_dilution100*glyc_C7_mean_conc100), - glyc_D2_dilution, glyc_D2_mean_lum, glyc_D2_mean_conc, (glyc_D2_dilution*glyc_D2_mean_conc), - glyc_E4_dilution, glyc_E4_mean_lum, glyc_E4_mean_conc, (glyc_E4_dilution*glyc_E4_mean_conc), - glyc_E5_dilution, glyc_E5_mean_lum, glyc_E5_mean_conc, (glyc_E5_dilution*glyc_E5_mean_conc), - glyc_E6_dilution, glyc_E6_mean_lum, glyc_E6_mean_conc, (glyc_E6_dilution*glyc_E6_mean_conc), - glyc_E7_dilution, glyc_E7_mean_lum, glyc_E7_mean_conc, (glyc_E7_dilution*glyc_E7_mean_conc)), ncol=4, byrow=TRUE) -colnames(tab) <- c('Dilution factor','Luminescence','Calculated Glycogen (ug/uL)', 'Total glycogen (ug/uL)') +wt_C7 <- get_weight_from_label(plate_layout[1, 1]) +wt_D2 <- get_weight_from_label(plate_layout[3, 1]) +wt_E4 <- get_weight_from_label(plate_layout[4, 1]) +wt_E5 <- get_weight_from_label(plate_layout[5, 1]) +wt_E6 <- get_weight_from_label(plate_layout[1, 4]) +wt_E7 <- get_weight_from_label(plate_layout[2, 4]) + +tab <- matrix(c(glyc_C7_dilution50, glyc_C7_mean_lum50, glyc_C7_mean_conc50, (glyc_C7_dilution50*glyc_C7_mean_conc50), (glyc_C7_dilution50*glyc_C7_mean_conc50*homogenate_volume_uL)/wt_C7, + glyc_C7_dilution100, glyc_C7_mean_lum100, glyc_C7_mean_conc100, (glyc_C7_dilution100*glyc_C7_mean_conc100), (glyc_C7_dilution100*glyc_C7_mean_conc100*homogenate_volume_uL)/wt_C7, + glyc_D2_dilution, glyc_D2_mean_lum, glyc_D2_mean_conc, (glyc_D2_dilution*glyc_D2_mean_conc), (glyc_D2_dilution*glyc_D2_mean_conc*homogenate_volume_uL)/wt_D2, + glyc_E4_dilution, glyc_E4_mean_lum, glyc_E4_mean_conc, (glyc_E4_dilution*glyc_E4_mean_conc), (glyc_E4_dilution*glyc_E4_mean_conc*homogenate_volume_uL)/wt_E4, + glyc_E5_dilution, glyc_E5_mean_lum, glyc_E5_mean_conc, (glyc_E5_dilution*glyc_E5_mean_conc), (glyc_E5_dilution*glyc_E5_mean_conc*homogenate_volume_uL)/wt_E5, + glyc_E6_dilution, glyc_E6_mean_lum, glyc_E6_mean_conc, (glyc_E6_dilution*glyc_E6_mean_conc), (glyc_E6_dilution*glyc_E6_mean_conc*homogenate_volume_uL)/wt_E6, + glyc_E7_dilution, glyc_E7_mean_lum, glyc_E7_mean_conc, (glyc_E7_dilution*glyc_E7_mean_conc), (glyc_E7_dilution*glyc_E7_mean_conc*homogenate_volume_uL)/wt_E7), ncol=5, byrow=TRUE) +colnames(tab) <- c('Dilution factor','Luminescence','Calculated Glycogen (ug/uL)', 'Total glycogen (ug/uL)', 'Normalized glycogen (ug/mg tissue)') rownames(tab) <- c('C7_df50','C7_df100','D2','E4','E5','E6','E7') tab <- as.table(tab) tab @@ -869,14 +886,14 @@ for (i in 1:nrow(glucose_summary_data)) { ``` ```{r, sample glucose calculations} -tab <- matrix(c(glu_C7_dilution50, glu_C7_mean_lum50, glu_C7_mean_conc50, (glu_C7_dilution50*glu_C7_mean_conc50), - glu_C7_dilution100, glu_C7_mean_lum100, glu_C7_mean_conc100, (glu_C7_dilution100*glu_C7_mean_conc100), - glu_D2_dilution, glu_D2_mean_lum, glu_D2_mean_conc, (glu_D2_dilution*glu_D2_mean_conc), - glu_E4_dilution, glu_E4_mean_lum, glu_E4_mean_conc, (glu_E4_dilution*glu_E4_mean_conc), - glu_E5_dilution, glu_E5_mean_lum, glu_E5_mean_conc, (glu_E5_dilution*glu_E5_mean_conc), - glu_E6_dilution, glu_E6_mean_lum, glu_E6_mean_conc, (glu_E6_dilution*glu_E6_mean_conc), - glu_E7_dilution, glu_E7_mean_lum, glu_E7_mean_conc, (glu_E7_dilution*glu_E7_mean_conc)), ncol=4, byrow=TRUE) -colnames(tab) <- c('Dilution factor','Luminescence','Calculated glucose (ug/uL)', 'Total glucose (ug/uL)') +tab <- matrix(c(glu_C7_dilution50, glu_C7_mean_lum50, glu_C7_mean_conc50, (glu_C7_dilution50*glu_C7_mean_conc50), (glu_C7_dilution50*glu_C7_mean_conc50*homogenate_volume_uL)/wt_C7, + glu_C7_dilution100, glu_C7_mean_lum100, glu_C7_mean_conc100, (glu_C7_dilution100*glu_C7_mean_conc100), (glu_C7_dilution100*glu_C7_mean_conc100*homogenate_volume_uL)/wt_C7, + glu_D2_dilution, glu_D2_mean_lum, glu_D2_mean_conc, (glu_D2_dilution*glu_D2_mean_conc), (glu_D2_dilution*glu_D2_mean_conc*homogenate_volume_uL)/wt_D2, + glu_E4_dilution, glu_E4_mean_lum, glu_E4_mean_conc, (glu_E4_dilution*glu_E4_mean_conc), (glu_E4_dilution*glu_E4_mean_conc*homogenate_volume_uL)/wt_E4, + glu_E5_dilution, glu_E5_mean_lum, glu_E5_mean_conc, (glu_E5_dilution*glu_E5_mean_conc), (glu_E5_dilution*glu_E5_mean_conc*homogenate_volume_uL)/wt_E5, + glu_E6_dilution, glu_E6_mean_lum, glu_E6_mean_conc, (glu_E6_dilution*glu_E6_mean_conc), (glu_E6_dilution*glu_E6_mean_conc*homogenate_volume_uL)/wt_E6, + glu_E7_dilution, glu_E7_mean_lum, glu_E7_mean_conc, (glu_E7_dilution*glu_E7_mean_conc), (glu_E7_dilution*glu_E7_mean_conc*homogenate_volume_uL)/wt_E7), ncol=5, byrow=TRUE) +colnames(tab) <- c('Dilution factor','Luminescence','Calculated glucose (ug/uL)', 'Total glucose (ug/uL)', 'Normalized glucose (ug/mg tissue)') rownames(tab) <- c('C7_df50','C7_df100','D2','E4','E5','E6','E7') tab <- as.table(tab) tab