I have been analyzing some single cell RNA sequencing data, which compares neural transcriptomes from mice treated with either vehicle, or a drug. All the basic stuff is going fine.
When I get my clusters, I find not many super interesting significant drug induced DEGs. If I do GSEA on each cluster, however, things look very interesting, and align with published literature very well. All good so far.
So my problem is this - I use fgsea in R to do my GSEAs, but I am doing the GSEAs on 18 different clusters. That means that my adjusted p values that I get from fgsea are not valid - they need to be corrected to reflect the 18 repeated tests.
If I were to Bonferroni correct those p values, would it be acceptable to take the fgsea output adjusted p values that were already corrected for the number of gene sets tested, and then correct them again? Or is it more appropriate to take the raw p value from fgsea and somehow Bonferroni it for both the number of gene sets tested and also the number of clusters in which I am performing the tests?
Basically, can you Bonferroni an adjp that has already been Bonferronied?
Thanks very much in advance for your insights! Ed