I'm doing a DE analysis with multiple conditions and I wondered what the right way is of doing so. For each comparison I'd only like to use a subset of the data. I wondered if it's possible to make one DESeq2 object and subset it for each comparison, for example like this:
dds <- DESeqDataSetFromMatrix(countData = cntmtx, colData = colData, design = ~ condition_A + condition_B) dds <- DESeq(dds) dds_sub_x <- dds[,dds$condition_A == "x"] res_sub_x <- results(dds_sub_x, contrast=c("condition_B","a","b"))
If condition_A has the levels of "x" and "y" and condition_B has the levels of "a" and "b".
Could someone tell me if it's alright to go about it like this?