Hello, I have raw p-values from edgeR for two comparisons of interest: control vs genotype1 and control vs genotype2. I'd like to see if there is an aggregate effect of genotype on DE.
The Internet has a number of answers on how to do a Fisher's combined test, and some resources on how to do this in R (such as the metaRNASeq package). But edgeR (as well as DESeq2) give two-sided p-values, while the R functions for combined tests requires a one-sided p-value. Does anyone know how to proceed? I'm also not sure if this is a valid way to get an aggregate result, since these two tests have the same control samples and are not independent. Does anyone have thoughts on whether it would be better to run the analysis in edgeR again, treating genotype1 and genotype2 as one group?