Hi,

I have this result in DESeq2:

> summary(res)

out of 60448 with nonzero total read count
adjusted p-value < 0.05
LFC > 0 (up)       : 7132, 12%
LFC < 0 (down)     : 6975, 12%
outliers [1]       : 751, 1.2%
low counts [2]     : 14064, 23%
(mean count < 3)
[1] see 'cooksCutoff' argument of ?results
[2] see 'independentFiltering' argument of ?results

Questions:

(1) There are many DEGs in this result. Is this percentage of upregulated (12%) and downregulated (12%) genes acceptable in DESeq2 analysis? Does it not violate the usual result?

(2) Also, I observed that LFC > 0 and LFC < 0 automatically appeared in the result by default. As most studies use higher than 0, is this threshold acceptable? Could it be the reason why I am having many DEGs?

Thank you!

Let me copy over my answers from GitHub

1. this is not a violation of the size factor calculation. check plotPCA, likely the groups are separated well
2. see the 2014 paper, or the vignette or workflow, you can use lfcThreshold and we recommend it