I did an analysis of RNA-seq using DESeq2 in Galaxy.
The problem is I have 3 conditions from one study and 3 from another study. They are not exactly the same conditions so I try to do a batch effect correction using RUV-seq.
Then I used it in DESeq2 (I used the “residual” method) but it does not seem to impact PCA at all (they superimpose) despite the fact that the table shows different numbers for each name and there was no error. Is it possible that there is no error but somehow the corrections did not apply (do I need the “condition” name to appear somewhere in DESeq2?
here first 6 are from one study, next 9 are from another study and I also tried to put the first 6 as condition batch 1 and the next 9 as condition batch 2 and it was the same (no change in PCA)
thanks a lot for your help