7.3 years ago by
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
edgeR has no difficulty with uneven library sizes, and will adjust for
this automatically for this during the analysis. There is no need for
to do anything other than follow a standard analysis pipeline.
You do not need to standardize the 4th sample by dividing the counts
dividing by 4, in fact you must not do this since it changes the
mean-variance relationship for your data and invalidates the
analysis. You need to input the true read counts into edgeR.
> 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
> I have replicate sample counts for 2 groups but one sample is 4x
number of mapped reads
> Than the other samples.
> I divided all the mapped transcript reads by 4 and then did the
> normalization and analysis With edgeR. What do you recommend to do
> the 4th sample counts?
> Lana Schaffer
> Biostatistics, Informatics
> DNA Array Core Facility
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