[BioC] deseq within and between group variation

[Simon Anders]

Dear Sudeep

On 2012-08-07 18:31, sudeep s wrote:

> Is there a way to calculate within and between group variability
> between two sample groups (with biological replicates) within DESeq ?
> I went through DESeq manual, but couldn't find any reference.  So is
> the only way is to calculate it directly from the normalized read
> count data ?

Count data is not homoscedastic and hence, there is no point in looking 
at within and between group variance or using other methods from 
standard linear regression methods. What you want is within and between 
group _deviance_, and these are calculated by the 'fitNbinomGLMs' 
function. Please read up in on generalized linear models (GLMs) and 
analysis of deviance (ANODEV).

   Simon