I'm quite sure I have a problem with the DESeq2 independent filtering. DESeq2 doesn't flag any outliers when performing the DE analysis. We have little concern about blood being in the samples as the raw counts vary from hundreds to tens of thousands in some HB related genes. For some reason DESeq2 doesn't get rid of these high count outlier genes which I think should appropriate. Or is possible for some genes to have such big variation in gene expression?
We have filtered out lowly expressed genes before the analysis but I think more filtering should be maybe manually done to get these high count outlier genes removed. When plotting the Q-Q-plot of p-values the trend a bit inflated which is a a slight concern also.
Help would be really appreciated because not quite sure how to approach this problem.