I used DESeq2 about 4 months back to analyse my data with the design:
with species A & B and condition 1 -5.
It gave resultsNames(dds) as:
"Intercept", "speciesA", "speciesB", "condition1"..."condition5", "speciesA.condition1"..."speciesB.condition5"
I used this to find various comparisons such as interaction effect of species and effect of any one condition against all others:
However, when I use DESeq2 now (yesterday) with the same design & dataset, I get different resultsNames(dds):
I have read the vignette help and understand these terms and that I can get different comparisons by releveling the reference factor. But I don't know how to get the data I could from the previous terms such as the comparison of one condition against groups of other conditions.
I think that this has to do with a change in the version of DESeq2 and someone updated the lab computer. Unfortunately I had not saved the sessionInfo() previously and don't know which version I had used. I would be grateful for any help regarding how I can get this information from these new terms, or even if I can go back to the old version with the previous terms since I am more familiar with them.
The current version I'm using is R version (3.2.3) and DESeq2_1.10.1