I've been looking in many topics, but none answer clearly my question. In a classical multiple groups RNA-seq analyse, does the flagging with the Cook's distance take in account the groups you're looking at?
Here's my experiement:
4 different groups (3 replicates, no batch effect, etc...)
res(dds, contrast=c('condition','group1','group2') )
I saw that a gene of interest was getting NA as pvalue and padj. To understand why, I decided to investigate on normalized count, raw count and Cook's distance. On the last metrics, one of the Group 3 samples is definitely considered as an outlier. So is that why I can't get pvalue for this gene, even if I'm currently working on the group 1 and 2, not the 3 ?
Has anyone a clue to avoid this effect ?