Hi,
I am using DESeq2 to get differential expression of 45 samples which
represent 26 different conditions.
I read that the calculation of the fold change in changed DESeq2 and
affects the genes having low counts more than the highly expressed genes.
However, I found genes that had zero counts in series of  4 samples (2
replicates in each of 2 conditions), while their log2fold change was 3.
what is the reason for that? or how can this be prevented?

I used the nbinomWaldTest and did not replace outliers with the trimmed
mean since I have only 2 replicates per condition.

I'd appreciate your help very much,
Noa Henig

	[[alternative HTML version deleted]]

