Making note of this -- no solution
If you rerun the workflow after dropping some samples (removing them from the samplesheet).
In make_sce.R, the dge is built from all ReadsPerGene.out.tab files with files <- list.files(star_dir, pattern = "ReadsPerGene.out.tab", full.names = FALSE)
this results in rows of NAs being introduced when the metadata subset to all samples with ReadsPerGene.out.tab data_for_DE <- data_for_DE[colnames(raw_cts), ]
because the original samples are not in the metadata, rows of NAs get introduced that causes this to give an error on the next line when stopifnot(all(!is.na(data_for_DE$group)))
Making note of this -- no solution
If you rerun the workflow after dropping some samples (removing them from the samplesheet).
In make_sce.R, the dge is built from all ReadsPerGene.out.tab files with
files <- list.files(star_dir, pattern = "ReadsPerGene.out.tab", full.names = FALSE)this results in rows of NAs being introduced when the metadata subset to all samples with ReadsPerGene.out.tab
data_for_DE <- data_for_DE[colnames(raw_cts), ]because the original samples are not in the metadata, rows of NAs get introduced that causes this to give an error on the next line when
stopifnot(all(!is.na(data_for_DE$group)))