Suppose I have a matrix of gene counts, whose rows represent genes, and columns represent samples. For RNA-seq packages such as edgeR and DEseq2, the counts are normalized and standardized before DE analysis.
My question is about the standardization itself. After normalizing each column to adjust for sequencing depth and library size, I calculate the log2(normalized counts + 1). Then, is each column further standardized (to get mean = 0 and standard deviation = 1), or is the standardization done on each row only?
Thank you for your help.