I've gone through and done all my contrasts for a rather large DE experiment using edgeR. I have logFC, logCPM, LR, PValue, and FDR for each of these contrasts but I can't figure out how to add a column that shows up/down regulation for each of my DEGs. I've tried extracting this information using
> updown.12Cvs24C<-decideTestsDGE(lrt.12Cvs24C, p.value=0.05)
and then adding this column to the results tables using cbind, but I don't think the up/down values are correctly corresponding to the right genes because I have a list of the DEGs (filtered for an FDR < 0.05) that show SAME (0) up/down regulation. If the FDR of these genes is < 0.05 (like the 6 genes shown below), it means that there expression was either significantly higher or lower in one group vs the other, yet the UpDown column doesn't reflect this.
geneID logFC logCPM LR PValue FDR UpDown
237542 -5.901809 2.871127 41.81711 1.002224e-10 5.653145e-07 0
1879515 -6.603091 5.203004 41.70325 1.062322e-10 5.653145e-07 0
1207284 -6.666918 4.879160 40.38631 2.083963e-10 7.393207e-07 0
131752 -5.096021 7.731907 37.80230 7.828952e-10 2.049564e-06 -1
29878 -6.932289 6.619459 37.25548 1.036232e-09 2.049564e-06 0
483711 -8.104056 7.199398 37.02868 1.164046e-09 2.049564e-06 0
Is there an easy way to extract this information and add it to the results table or do most people just infer it from the logFC values that are already present in the results table? FYI- not an R wiz so be gentle.
Bonus question (while i have your attention): Is there an easy way to isolate the DEGs that are similar between two groups (different contrasts). I know this can be done easily in Galaxy but I'd like to learn it in R. So far can't find a lot about this kind of action.