Hi, Could someone please tell me how to remove NAs from the DESeq2 pipeline? Even though I initially filtered out low expressed genes, I am getting NA values with the below code

Thank you

res_low_H1$sig <- as.factor(ifelse(res_low_H1$padj<0.05 & abs(res_low_H1$log2FoldChange)>2, 
                            ifelse(res_low_H1$log2FoldChange>2, "up", "down"), "not"))
summary(res_low_H1$sig)

#output
#down   not    up  NA's 
# 365 15366   398     8

Hi please read this section of the vignette: Why are some p values set to NA?.

Kevin