I have rna-seq data (18 samples) from which I produced the raw counts using htseq-count. Now I want to analyze the data using edgeR. I've done this dozens of times and had no issues. Not this time. When I execute
samples <- read.csv(file="metadata_composite.csv",header=TRUE,sep=",") counts <- readDGE(samples$CountFiles)$counts
Error in taglist[[i]] : subscript out of bounds
I've analyzed the same data using Deseq2 and had no issues whatsoever. So it is something related to edgeR. Here is my data - it consists of 18 directories each containing a count file (accepted_hits.count) and a directory called edgeR which contains "metadata_composite.csv" which is the metadata file that I load in in the code snippet above.
Can you tell what is the problem?