Because no matter how fancy the statistics is, we have to find something having biological significance. For example, in most time, even have p<0.000000000001, still get no biological effects.
For most gene expression change, people always use fold change 2 as a cutoff for microarray or qPCR. As for RNAseq, since the method is much more sensitive, I guess it must lose some specificity, so I think it may need a higher cutoff number than 2.



-----Original Message-----
From: bioconductor-bounces@r-project.org on behalf of Simon Anders
Sent: Tue 3/27/2012 5:14 AM
To: bioconductor@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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