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Old 09-09-2016, 03:55 AM   #1
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Default FDR Correction before gene ontology analysis


I am analysing some RNA-seq data. I get a gene list of differentially expressed genes with around 100 DE genes if the FDR value, rather than the raw P-value, is used.

When using this list of differentially expressed genes for gene set enrichment analysis should I be using the FDR values from the differentially expressed genes or the raw P values +/- a log fold change cut off.

I am thinking that it should be the FDR values from my differentially expressed genes but I have come across a few published papers in my field that have used a P-value and a log fold change cut off (although when I go back through the data from these studies they have very few differentially expressed genes by FDR so perhaps this is the reason).

Would be interested in your opinions on this.
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