Hi,
I have a simple case, design(dds) = ~ sex + batch + condition, where condition is a factor with three levels (A, B, and C). I tried two different ways of testing differential expressed genes between condition B and C:
Method 1: Run DEseq on the whole dataset, and extract comparison between B and C as results(dds, contrast = c("condition","B","C")).
Method 2: Subsetting the dataset by extracting samples only with condition B and C, relevel the condition, then run DEseq on the subset, get result via results(dds_subset, contrast = c("condition","B","C"))
I expected the two methods have same results, but actually they don't. I got different number of DE genes with the same FDR cutoff.
Anything I misunderstand? Please advise.
Thanks,
-Xianjun
This is also one of the FAQ in the vignette.