edgeR parameters
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6 weeks ago

I have a doubt regarding filtering results of edgeR I am not getting how to consider whether our genes which we got from edgeR are significant or not.We got 22,000 genes but I need to filter .The parameters set wereMin CPM =1, Log2fc=0,Pvalue adj=0.05. How should I know which genes are significant of these. enter image description here

edgeR ATAC-SEQ • 189 views
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The genes with an adjusted p-value below your alpha are indeed significant, but the other question you need to ask is what fold change value you would consider biologically interesting. It may be the case that a gene has a p-value below your alpha but a fold change of 5%, which is usually not terribly interesting, which is why magnitude of effect is equally as important. Most people will set a |log2FC| threshold of 1 for example since that corresponds roughly to a doubling or halving of expression.

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Thankyou for the reply.My FDR values (adjusted p values) are starting from 0.3 and above ,there is no values less than 0.05 in the FDR column.So does that mean all of my edgeR results are not significant.

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