[BioC] uneven counts for edgeR

[Lana Schaffer]

Gordon,
Thank you for this information.
Is the same true for DeSeq?
Lana

-----Original Message-----
From: Gordon K Smyth [mailto:smyth at wehi.EDU.AU] 
Sent: Saturday, October 22, 2011 5:42 PM
To: Lana Schaffer
Cc: Bioconductor mailing list
Subject: uneven counts for edgeR

Dear Lana,

edgeR has no difficulty with uneven library sizes, and will adjust for 
this automatically for this during the analysis.  There is no need for you 
to do anything other than follow a standard analysis pipeline.

You do not need to standardize the 4th sample by dividing the counts by 
dividing by 4, in fact you must not do this since it changes the 
mean-variance relationship for your data and invalidates the subsequent 
analysis.  You need to input the true read counts into edgeR.

Best wishes
Gordon


> Date: Fri, 21 Oct 2011 15:27:25 -0700
> From: Lana Schaffer <schaffer at scripps.edu>
> To: "'bioconductor at r-project.org'" <bioconductor at r-project.org>
> Subject: [BioC] uneven counts for edgeR
>
> Hi,
> I have replicate sample counts for 2 groups but one sample is 4x number of mapped reads
> Than the other samples.
> 528,428
>
> 625,889
>
> 498,569
>
> 2,328,333
>
> I divided all the mapped transcript reads by 4 and then did the 
> normalization and analysis With edgeR. What do you recommend to do with 
> the 4th sample counts?
>
> Lana Schaffer
> Biostatistics, Informatics
> DNA Array Core Facility
> 858-784-2263

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