[BioC] deseq for multiple groups with no replicate

[Wolfgang Huber]

Dear Yolande

Thanks. Can you clarify what you want to do:
- per gene: ANOVA like estimation of effects in a factorial design
- per sample: clustering or classification of samples based on overall 
(dis)similarity of expression profiles?

 From your post, I assume it's the latter. This is described in Section 
"Sample Clustering" of the vignette.

(For the former, there are the functions nbinomFitGLM and nbinomGLMTest, 
but these will with the current implementation of DESeq only work if 
each cell of the design is replicated.)

	Thank you and best wishes	
	Wolfgang

Yolande Tra scripsit 04/04/11 00:49:
> Dear list members,
>
> I would like to know if it is possible to use deseq for data with multiple
> groups (more than two) with no replicates. I went through the vignette but
> it only illustrates the case for two groups with no replicates. If it is not
> possible for the moment, do you know a method to study
> similarity/dissimilarity of gene/protein count data based on multiple groups
> with no replicates.
>
> I appreciate your feedback.
>
> Yolande
>
> 	[[alternative HTML version deleted]]
>
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-- 


Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber