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Add tissue weight normalization to glycogen assay analysis #2

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Initial plan
Copilot Mar 19, 2026
a54549d
Add tissue weight normalization to all production glycogen assay Rmd …
Copilot Mar 19, 2026
42c30db
Fix glucose column headers: correct units from uM to ug/uL in 2026012…
Copilot Mar 19, 2026
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65 changes: 43 additions & 22 deletions Glycogen/code/Gen5-20260123-mgig-glycogenglo.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -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: "<sampleID>-<type>-<weight>-df.<dilution>", 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)
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down
60 changes: 38 additions & 22 deletions Glycogen/code/Gen5-20260126-mgig-glycogenglo.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -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: "<sampleID>-<type>-<weight>-df.<dilution>", 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)
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand Down
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