[BioC] Up & Downregulated genes using DESeq

Ekta Jain Ekta_Jain at jubilantbiosys.com
Tue Mar 27 12:46:45 CEST 2012


I am not a statistician but from whatever experience i have had to find differentially expressed genes, the logFC cut off used has been of a two-fold change (increase or decrease). Of course, if in any analysis your fold change gene list needs be reduced or increased for number of genes you could change the two-fold threshold to zero or three.

For a first off step, arbitrarily (as bruce also put it), two fold change seems ideal to use.

Best,
--E



-----Original Message-----
From: bioconductor-bounces at r-project.org [mailto:bioconductor-bounces at r-project.org] On Behalf Of Bruce Moran(External)
Sent: 27 March 2012 15:07
To: Simon Anders; bioconductor at r-project.org
Subject: Re: [BioC] Up & Downregulated genes using DESeq

Would be very interested to know how to define a fold change cutoff for
RNAseq data. Doesn't seem to be any power analysis that might be of use.

I use 2 (arbitrarily) also.

Bruce.

-----Original Message-----
From: bioconductor-bounces at r-project.org
[mailto:bioconductor-bounces at r-project.org] On Behalf Of Simon Anders
Sent: 27 March 2012 10:15
To: bioconductor at r-project.org
Subject: Re: [BioC] Up & Downregulated genes using DESeq

On 03/27/2012 06:34 AM, Ekta Jain wrote:
> As far as i gather, the threshold for upregulated or downregulated
genes should be>2FoldChange and>-2 FoldChange respectively. Not>0 or<0.

Why 2?

   Simon

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