[BioC] DESeq and paired samples - pairing vs pooling

[Martin Morgan]

On 05/21/2011 07:10 AM, Timothy Hughes wrote:
> Hi,
>
> We are performing a study of 8 individuals with cancer. We have 8 pairs of
> samples. Each pair consists of two samples from the same individual: one
> from cancerous tissue and one from normal tissue.

Hi Tim -- not really answering your question with respect to DESeq, but 
section 11 of the edgeR manual walks through a paired design. Martin

>
> We have used DESeq to perform a pooled comparison between the normal and
> cancerous samples and find a number of genes that are differentially
> expressed.
>
> We would also like to perform a paired analysis (simple comparison between
> the two tissue samples from the same individual). Our logic is that the
> pooled analysis will tend to identify genes as differentially expressed only
> if they are fairly consistently up or down-regulated across individuals.
> But, the etiology of the same cancer type may be heterogeneous and we aim to
> investigate this by performing the paired analysis. In connection with this,
> I have two questions:
> 1. we read in the DESeq paper that this can be done, but are we correct in
> believing that we can interpret the results as I describe above?
> 2. Does it make sense to do a paired analysis as described above or would it
> make more sense to pool the normal tissues and then compare each cancerous
> tissue to the pool?
>
> Thanks for your help.
>


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