Hi, I used DESeq2 to analysis read count data using LRT test. I have multiple covariates in the GLM model. But my MAplot and dispersion plot do not look like typical plots in the manual. Also the histogram of raw p value have a high peak on 1.
Does it indicate a problem of model fitting? Do I need to discard the low-count transcript first? Also how "good" do the MAplot and dispersion plot need to be, in order to claim a properly fitted model?