[BioC] edgeR : How to associated trait with DE?

[Gordon K Smyth]

Dear Sermsawat,

In edgeR, you can simply add a quantitative column to the design matrix, 
then use glmFit() and glmLRT() to test for the significance of the 
coefficient for that column.

I do not recommend that you do the calculations using the pseudo counts.

Best wishes
Gordon

> Date: Tue, 13 Sep 2011 23:01:29 -0400
> From: Sermsawat Tunlaya-anukit <stunlay at ncsu.edu>
> To: bioconductor at r-project.org
> Subject: [BioC] edgeR : How to associated trait with DE?
>
> Can i associated trait into edgeR result? I have quantitative traits 
> such as height in each library that would like to find gene that 
> co-regulate or co-expression with that trait. How can i apply this into 
> edgeR? Can i use $psedo.alt to calculate correlation with my trait? Or i 
> should GLM to calculate DE that associated with trait? I am not sure how 
> to apply my trait into design or another vector and calculate 
> estimateGLMCommonDisp.
>
> Thank in advance,
> Sermsawat Tunlaya-anukit

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