I have 10 strains with three replicates grown under the same condition. I would like to perform pairwise comparisons between the 10 strains without repeating. Within Deseq2, setting up all possible individual contrasts takes up a lot of time. I was wondering if there is a faster way to perform this operation and save the result files.
Only run DESeq() once, then use results(dds, contrast=c("condition","B","A")) to compare two groups.
For performing all pairs of the 10 groups (45 pairs), you really need take into consideration that you are doing multiple testing in terms of contrasts as well as genes. The limma User's Guide has some recommendations for options there are (see section 13.3 Multiple Testing Across Contrasts). I would recommend you do a "global" correction, as described there.
We don't have functions to do this in DESeq2, because it's rare that someone wants to perform so many contrasts. What you should do to perform a global correction is to make a vector of all the p-values from all the contrasts, then use p.adjust(..., method="BH") to adjust them, then you can reassign to the different tables. If this is confusing, you might want to talk to a bioinformatician or data analyst who can help you to perform these corrections.
Thank you for the recommendation above!
I read through Limma's user guide. It is stated that method="global" is recommended when a set of closely related contrasts are being tested. It appends all the tests together into one long vector of tests, i.e., it treats all the tests as equivalent regardless of which contrast they relate to. I have one question if that's ok. I have 10 age groups and I want to do pairwise comparisons (so in total 45 comparisons), assuming I named my age groups as Ages A - I. It should be as
So, here I am performing every contrast separately, running it one by one .. In this case, why would I use method="global"? Shouldn't I use method="separate" since I am running these comparisons separately and retrieving the adj-p values separately?
We only provide the adjustment per comparison in DESeq2.
Thank you, Michael for your quick reply! Sorry but I am still confused. Are you saying that I can use the method="separate" since we are doing every contrast separately?
Hi Michael, just wanted to follow up on my previous question if that's ok :) ... Are you confirming that method='separate" can be used since I am running every contrast separately?
Yes that is how we approach multiple testing