[BioC] EdgeR glm based analysis

Gordon K Smyth smyth at wehi.EDU.AU
Thu Jan 2 04:33:37 CET 2014

Dear Reema,

Yes, you can use the glm based analysis for two groups.  The results will 
be similar to using the exact test, but the p-values will be based on an 
asymptotic approximation rather than being exact.

Best wishes

> Date: Tue, 31 Dec 2013 20:47:31 +0000
> From: Reema Singh <reema28sep at gmail.com>
> To: bioconductor <bioconductor at r-project.org>,	Bioconductor mailing
> 	list <bioconductor at stat.math.ethz.ch>
> Subject: [BioC] EdgeR glm based analysis
> Dear All,
> First, wish you all a very happy and prosporous New Year.
> In EdgeR manual[Case Studies section], for two group comparison, generally
> exactTest usage is shown, whereas for the multiple group comparison glm
> based analysis has been shown. In 1.4 quick start section, use of glm based
> analysis for two group comparison is mentioned with an additional use of
> design matrix.
> Now my question :- Is it ok to use glm based analysis for two group
> comparison? I would appreciate any suggestion.
> Kind Regards
> -- 
> Reema Singh
> Postdoctoral Research Assistant
> College of Life Sciences
> University of Dundee,
> Dundee DD1 4HN, Scotland
> United Kingdom

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