Dear all, I'm using edgeR for differential analysis of ChIPseq data between two group (3 samples for each group). All is fine up to TMM normalization (I have understand how the norm factor are calculated) but starting from this point my nightmare start.
I can't understand how my count matrix are used by estimateDisp, glmQLFit and glmQLFTest functions.
Can some of you explain in the easier way as possible (showing a matrix and showing how to calculate dispersion gene by gene) in order to better understand these steps?? Also tutorials where matrix and how to use it are shown could be helpful User guide is well written but I can't understand how 3 mentioned functions works.
Lot of beer for who will stop my nightmare
Thanks a lot