I am using limma-voom to determine the change in the change of gene expression between men and women due to a treatment. I have previously received great help on this site, and am confident in my workflow up until choosing a method to do multiple testing correction int he decideTests method. I don't understand the minutia defining each option, and am hoping someone can help me choose the most appropriate method.
My contrast matrix is as follows: makeContrasts(M.PvP="fMale.post-fMale.pre", F.PvP="fFemale.post-fFemale.pre", sexDiff="(fFemale.post-fFemale.pre) - (fMale.post-fMale.pre)", levels = design)
I am interested in the contrast of the contrasts: sexDiff. From researching my issue I've come to appreciate that multiple testing correction across contrasts is complicated and way over my head. When I gather my results using decideTests(), should I specify for the correction method "separate", "global", "nestedF", or "hierarchical"? (https://bioconductor.org/packages/release/bioc/manuals/limma/man/limma.pdf pg.50)
Any help would be greatly appreciated! Thank you!