Hello, after using DESeq2 to analyze my dataset, I called the following code to count the number of genes with adj pvalue<0.05. However, when I export the data, the number of genes with adj pvalue<0.05 in the spreadsheet is much lower than that (125). I exported right after the above code, so no more data filtering/transformation was applied.

> ##using p=0.05
> res05 <- results(dds, alpha=0.05)
> summary(res05)

out of 45412 with nonzero total read count
adjusted p-value < 0.05
LFC > 0 (up)       : 2626, 5.8%
LFC < 0 (down)     : 2197, 4.8%
outliers [1]       : 270, 0.59%
low counts [2]     : 7801, 17%
(mean count < 13)
[1] see 'cooksCutoff' argument of ?results
[2] see 'independentFiltering' argument of ?results

> 
> sum(res05$padj < 0.05, na.rm=TRUE)
[1] 4823

Anybody has any idea why that is happening?

Thank you!

I don't know how you are counting adj p-value < 0.05 outside of R, could it be there is a mistake on that end?