I'm dealing with and RNA-seq experiment with a total of 11 different conditions.
I'd like to do pairwise comparisons between some of them (without having a fixed base/ctrl condition). To do that, I'm planning to use the Wald-test.
After setting conditions (n=11), this is the command I used (in this example I want to compare condition C to E)
dds <- DESeqDataSetFromMatrix(countData = cts, colData = colData, design = ~ 0 + condition) dds <- DESeq(dds) res_condC_versus_condE = results(dds, contrast=c("condition","condC","condE"))
I've two main questions:
- Do you think the design formula and the results command are set in the correct way?
- Should I use lfcShrink only for data visualization and ranking??
Thank you for your time!!