Re: warning with lmFit command in limma

Thanks Smith.

-----Original Message-----
From: Gordon K Smyth [mailto:[email protected]] 
Sent: 09 August 2014 05:02
To: Marwaha, Shruti (marwahsi)
Cc: Bioconductor mailing list
Subject: warning with lmFit command in limma

Your design matrix looks correct on my quick look.

Gordon


> Date: Thu, 7 Aug 2014 15:05:12 +0000
> From: "Marwaha, Shruti (marwahsi)" <[email protected]>
> To: "[email protected]" <[email protected]>
> Cc: "smyth-QpO9qclcJEu6c6uEtOJ/[email protected]" <smyth-QpO9qclcJEu6c6uEtOJ/[email protected]>
> 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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