Hi there,

Apologies if this is a naive question, I'm fairly new to this and I'm not sure I've interpreted the vignette appropriately.

I've ran DESeq2 on a dataset that includes around 30 conditions - which means there's a lot of comparisons that can be gathered.

I'm only interested in a few of these comparisons, so I'm only taking a few further for high level analysis.

However, I've been told that I should correct the results of the DESeq2 because there's a number of different tests (comparisons) being used in DESeq2.

I wasn't sure if this seemed correct - or if running a DESeq2 on all the data when I'm only interested in a few comparisons is appropriate.

Hope this makes sense, I can give extra context if required! Thanks for any help in advance!

It's not clear exactly what you are asking, but I infer that you are asking about correcting for multiple comparisons. This has to do with the number of genes rather than the number of conditions (I mean technically you should adjust for all the comparisons that you made, but it seems most people just adjust within each comparison). And DESeq2 automatically includes the adjusted p-values that account for multiple comparisons, so it is all handled for you.