Question

Counterintuitive results from edgeR

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Son Pham ▴ 60

@son-pham-6437

Last seen 9.9 years ago

United States

Hi edgeR community: I'm testing for DE genes in two groups. Group A has 6 replicates, group B has 4 replicates. I spot a very strange gene, that should be DE but somehow edgeR doesn't report it. Here is the log2CPM of group A: (5.8804275247607; 5.95666869234362; 6.24683910018322; 4.03634160591149; 4.9390167413036; 5.22009594582392) and log2CPM of group B: (6.68129783945799; 6.31414609301072; 6.94357946236393; 6.19026250939524) It's clear for us that these two groups has different CPM: B > A. But here is how edgeR reports: MyGeneID 0.990998868329884(logFC) 6.11753790162748(LogCPM) 0.0238675732815782(Pvalue) 1(FDR). This is very counter intuitive. Why here we have FDR = 1 ? and even I can not infer how logFC = 0.99 Any clarification is greatly appreciated ! Thank you, Son. [[alternative HTML version deleted]]

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ADD COMMENT • link updated 10.6 years ago by Gordon Smyth 52k • written 10.6 years ago by Son Pham ▴ 60

score 0 · Answer 1 · 2014-04-19

Dear Son,

I am not seeing anything counterintuitive here.

edgeR gives you a P-value of 0.02 for this gene, which agrees perfectly with your intuition that the gene looks differentially expressed if considered in isolation.

The logFC is reported to be 0.99, which looks pretty similar to the change in average logCPM from group A to group B. This all seems as expected.

The reason for FDR=1 is that, given the number of genes in your experiment and given the variability in your experiment, you could easily fish around in the data to find a gene that looks as DE as this one, even if there
were in fact no truly DE genes. This is the difference between testing for DE for one gene in isolation, versus adjusting for multiple testing over thousands of genes.

In general, you should not expect a gene with a modest p-value like 0.02 to be chosen as significantly DE after adjusting for multiple testing over tens of thousands of genes.

Best wishes
Gordon