Hi,

I would like to do differential expression analysis of one group of samples (miRNA) against all samples in the dataset (e.g samples A,B,C, against samples A...K ). At the moment I have tried to use DESeq2 for this purpure. I did not find description of such possibility in DEseq2 manual, however it did not give me any errors while I was doing that. My question is if it is OK to use DESeq2 in such way, or there are perhaps some better options?

I think it would be better to do a contrast of A,B,C against samples D...K  If you include e.g. sample A in the model twice (as it appears you are doing), then the residuals aren't going to be independent, which is one of the key requirements of regression. If there's a valid reason for including the sample in both groups (and I can't think of one), then there's no simple alternative to DESeq that will deal with correlated residuals any better.  You'd need to get statistical advice on how best to deal with the correlation in your specific case, but the easiest route to removing the problem is to split the samples disjointly.