[BioC] deseq for multiple groups with no replicate

[Simon Anders]

Hi Yolanda

On 04/04/2011 03:42 PM, Yolande Tra wrote:
> I do have protein count data for 40 people (so no replicate). These are
> healthy people, no grouping. The goal is to look at similarity/dissimilarity
> of the 40 samples based on protein count (differential expression IF
> POSSIBLE) AND clustering of the proteins. As you said, clustering of samples
> can be done with the section "Sample Clustering" of the vignette. How would
> I go for clustering the proteins and look for differential expression (IF
> POSSIBLE).

The whole point of DESeq is to allow you to work in a small sample-size 
setting, where you need to pool data from several genes to get useful 
dispersion estimates.

With 40 people, you are beyond that, and you can use any conventional 
tests that are suitable for overdispersed count data.


I don't quite know what you mean by differential expression in this case 
anyway. No two persons will have the same protein level, so everything 
is differentially expressed in some way.

Maybe, you may want to estimate the variance of the proteins and look 
for strongly varying versus weakly varying ones. Supplementary Note A of 
our paper on DESeq describes a simple method-of-moments estimate for the 
biological variance that subtracts the Poisson noise and deals with 
different sequencing depths.

For a discussion of the clustering, DESeq's variance-stabilizing 
transformation might help for clustering genes in a similar way as for 
clustering samples.

   Simon