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Old 09-09-2016, 04:55 AM   #1
TAR76
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Location: UK

Join Date: Jun 2015
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Default FDR Correction before gene ontology analysis

Hi,

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.
Thanks.
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