[BioC] warning with lmFit command in limma

Gordon K Smyth smyth at wehi.EDU.AU
Sat Aug 9 11:01:42 CEST 2014

Your design matrix looks correct on my quick look.


> Date: Thu, 7 Aug 2014 15:05:12 +0000
> From: "Marwaha, Shruti (marwahsi)" <marwahsi at mail.uc.edu>
> To: "bioconductor at r-project.org" <bioconductor at r-project.org>
> Cc: "smyth at wehi.edu.au" <smyth at wehi.edu.au>
> Subject: Re: [BioC] warning with lmFit command in limma
> Thanks Smith for your quick response. Thanks for pointing out the log2 
> transformation problem in my code. You are correct, I was following 
> GEO2R code.
> I will also like to confirm with you if my design matrix is correct for 
> a two color experiment with common reference where the samples are 
> paired (cancerous and adjacent noncancerous tissues were obtained from 
> same patient).
> Thanks & Regards,
> Shruti Marwaha
> Graduate Student
> Systems Biology and Physiology
> University of Cincinnati
> Medical Science Building,
> 231 Albert Sabin Way
> Cincinnati, OH, USA 45267

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