I have couple of questions
1. The number of differentially expressed genes shot almost 6 fold (from ~1000 to ~6000) between deseq and deseq2. Is this a common trend and if so, why?
2. For gene, the raw counts are as follows (control - 0,10,670; treatment - 12986,9118, 6409). But the results looks like this. NAs are generated because of one zero value in the control? I thought pseudo counts are added if the counts are zero.
baseMean log2FoldChange lfcSE stat pvalue padj
3331.195751 4.6590639 1.2223685 3.8115050 NA NA
when I converted the ZEROs to ONEs pvalues are as follows...and the number of differentially expressed genes also reduced.
4076.763438 4.29728935 0.9134027 4.70470420 2.542343e-06 6.884325e-05