due to a strange error in DESeq my group is finally being forced to switch to DESeq2 (probably a good thing). There is one problem we are not sure how to solve, though:
In the old DESeq, we would normalise the data and then call nbinomTest() for each comparison we wanted to make. Now, the DESeq() function does all in one, which is nice up until you don't want to compare everything with everything else. We have a data frame with over 400 samples and only want to compare them to the wild type, not to each other. I can't find any possibility to do so, though, neither with DESeq() nor with nbinomWaldTest().
Is it in this case recommended to reduce the data set before using DESeq2, for each comparison, or should we try to run the DESeq() function once and then save it to extract only the relevant results?