[BioC] DESeq questions

Simon Anders anders at embl.de
Tue Dec 7 15:29:02 CET 2010

Hi Shrey

regarding your other question

On 12/06/2010 10:54 PM, Shreyartha Mukherjee wrote:
> I have RNA-seq count data for 30,400 genes across 6 conditions (3 replicates
> per condition). I was trying different normalization methods and then test
> for differentially expressed genes between conditions. How to test whether
> estimateSizeFactors() and estimateVarianceFunctions() does a good fit for my
> data? Also is there a way to test whether the normalization is good ? Any
> help is greatly appreciated,

To check the effect of estimateVarianceFunctions: have a look at the 
package vignette, specifically at Fig. 2. There, the variance estimates 
for each gene are plotted against the mean, and the estimated variance 
function is indicated by a red line. This should show a reasonable fit.


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