[BioC] DEseq for paired samples

Devon Ryan dpryan at dpryan.com
Fri Aug 30 08:39:43 CEST 2013

Hi Prabhakar,

The general method you're looking for is to add "patient" (or whatever term you prefer) as a factor in your design. So, if you denote tumor/normal by a factor called "status":

counts ~ status + patient

would likely be the formula you want. You could also allow an interaction if it makes sense for your dataset, by swapping an asterisk for the plus sign. You'll need to specify the individual patients in your dataframe, of course.


Devon Ryan, Ph.D.
Email: dpryan at dpryan.com
Molecular and Cellular Cognition Lab
German Centre for Neurodegenerative Diseases (DZNE)
Ludwig-Erhard-Allee 2
53175 Bonn, Germany

On Aug 30, 2013, at 12:12 AM, Prabhakar Chalise wrote:

> Hi,
> I was looking for a method to identify differentially expressed genes using the paired tumor/normal samples. Is there a method under DEseq to test for such correlated data?
> Thanks,
> -Prabhakar Chalise
> 	[[alternative HTML version deleted]]
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