Lower FDR cutoff gives more gene counts
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Binjie • 0
@2834fbcf
Last seen 11 weeks ago
United States

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

DESeq2 • 212 views
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Entering edit mode
@mikelove
Last seen 1 minute ago
United States

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.

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