[BioC] edgeR: calcNormFactors question

[Belinda Phipson]

Hi Gowthaman

Your output looks fine. What is more important is that library size is taken into account as an offset later on when you fit the glm. See help(glmFit).

Cheers,
Belinda

-----Original Message-----
From: bioconductor-bounces at r-project.org [mailto:bioconductor-bounces at r-project.org] On Behalf Of gowtham
Sent: Friday, 22 June 2012 9:40 AM
To: bioconductor
Subject: Re: [BioC] edgeR: calcNormFactors question

Sorry about repeated mailing: I have attached a smear plot of the data incase that helps anyone attempting to answer my doubt.....


On Thu, Jun 21, 2012 at 4:07 PM, gowtham <ragowthaman at gmail.com> wrote:

> Hi Everyone,
> I am analyzing a RNAseq experiment with two groups each having two 
> replicates. One out of 4 libraries have only half as much reads 
> mapping to genome.
>
> Lib Fe+.1 has only 4 million reads while other are 9 million +. But 
> still the norm.factors are not much different. With my naive 
> understanding i expect Fe+.1 to be very different from others. I would 
> like to know if what I see is okay?
>
> > oldsetDGE <- calcNormFactors(oldsetDGE) oldsetDGE$samples
>       group lib.size norm.factors
> fe-.1     2  9664343    0.9865411
> fe-.2     2 11248827    1.0812947
> fe+.1     1  4194124    0.9662389
> fe+.2     1  9963626    0.9701888
>
>
> Thanks very much,
> Gowthaman
> --
> Gowthaman
>
> Bioinformatics Systems Programmer.
> SBRI, 307 West lake Ave N Suite 500
> Seattle, WA. 98109-5219
> Phone : LAB 206-256-7188 (direct).
>



--
Gowthaman

Bioinformatics Systems Programmer.
SBRI, 307 West lake Ave N Suite 500
Seattle, WA. 98109-5219
Phone : LAB 206-256-7188 (direct).


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