Do we need to correct any of the data from DESeq2, if we only want to investigate some of the comparisons?
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smac97 • 0
@8eea9978
Last seen 17 hours ago
United Kingdom

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!

DESeq2 correction • 98 views
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@james-w-macdonald-5106
Last seen 7 hours ago
United States

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.

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Apologies for it not being clear, and thanks for getting back to me! The part that was confusing me was the side-note you make about adjusting for all comparisons - this was what I was told to do but having never done this before I was confused. So it is possible to adjust within a comparison? Do you know of any resources explaining how to do this (or possibly expand upon it more yourself)? Thanks again for your help, and sorry if I'm more unclear / naive!

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