Hi everyone, I am new to DESeq2. When I adjusted the alpha value in results() function, I found that when alpha=0.05, the number of genes with adjust p value < 0.05 is 2452, whereas when alpha=0.1, the number of genes with adjust p value < 0.1 is 2082. I am very confused with the results, because I thought with lower alpha value, the number of genes should be smaller. Probably I didn't understand the tool correctly. But I really appreciate anyone giving some thoughts, advice, or clues. Thanks!!

dds <- DESeq(dds)
res <- results(dds, contrast=c("disease","aortic stenosis","none"))
summary(res)
sum(res$padj < 0.1, na.rm=TRUE)

sum(res$padj < 0.1, na.rm=TRUE) [1] 2082

res05 <- results(dds, alpha=0.05)
summary(res05)
sum(res05$padj < 0.05, na.rm=TRUE)

sum(res05$padj < 0.05, na.rm=TRUE) [1] 2452

These are separate optimizations (setting alpha determines the target for independent filtering), so this can happen.

The second one did more filtering of low counts genes, see summary.