[BioC] What is difference between classic and GLM edgeR

[Gordon K Smyth]

Dear Sara,

Well, the exactTest is applicable in this case, so it would be logical to 
use it.  But both the classic exactTest and the more general glm 
approaches will give similar results.

You don't mention having read any documentation but I presume that you 
must have read the edgeR User's Guide.  The first three case studies in 
the User's Guide are two group comparisons, and they all use the 
exactTest.

Best wishes
Gordon




> Date: Tue,  6 Nov 2012 05:47:20 -0800 (PST)
> From: "sara [guest]" <guest at bioconductor.org>
> To: bioconductor at r-project.org, swilsonn86 at gmail.com
> Subject: [BioC] What is difference between classic and GLM edgeR
>
>
> Dear list,

> I have an RNA seq experiment data and I intend to extract differentially 
> expressed genes for my data. The data is from two groups(male and 
> female) and I want to know which genes are DE between this two groups. 
> Which approach of edgeR should I use? The classic one with exactTest 
> function or the GLM approach.

> Thank you for your reply
>
> -- output of sessionInfo():
>
> Thank you for your reply
>

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