[BioC] deseq for multiple groups with no replicate

[Simon Anders]

Hi Yolanda

On 04/04/2011 07:34 PM, Yolande Tra wrote:
> For clustering the proteins what would be conds (defined in the
> vignette) in
> cds3<-newCountdataSet(countsTable,conds)
> since there are many proteins with no specific condition.

Just put something, e.g.,

    cds3 <- newCountDataSet( countsTable,
       rep( "dummy", ncol(countsTable) )

This assigns the same condition to all of them. Of course, you cannot 
use the 'nbinomTest' function, if you have only one condition, but that 
wouldn't make sense anyway.

> In the vignette there were two conditions: "N" and "T".
> For three different people (not 40), how you would define the cds in the command
> res<=nbinom(cds,"N","T").

In a contrast, you compare two condition. In the vignette example, we 
ask: Is the expression in "T" stronger or weaker than in "N"?

How would you generalize such a question to three conditions? I don't 
see what other option there is than to make three pair-wise comparisons 
-- unless you want to go away from the "which condition has the stronger 
expression?" kind of question to some other hypothesis formulation.

   Simon