[BioC] deseq within and between group variation
anders at embl.de
Wed Aug 8 18:55:07 CEST 2012
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).
More information about the Bioconductor