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  : 270, 0.59% low counts  : 7801, 17% (mean count < 13)  see 'cooksCutoff' argument of ?results  see 'independentFiltering' argument of ?results > > sum(res05$padj < 0.05, na.rm=TRUE)  4823
Anybody has any idea why that is happening?