[BioC] calcNormFactors - normalization

[Lana Schaffer]

Mark,
My gene library contains only 141 genes.  Is this low number
Alright in this model?
The length on the genes are not accounted for in this package edgeR?
Lana

-----Original Message-----
From: Mark Robinson [mailto:mrobinson at wehi.EDU.AU] 
Sent: Friday, May 06, 2011 4:55 PM
To: Lana Schaffer
Cc: 'bioconductor at r-project.org'
Subject: Re: [BioC] calcNormFactors - normalization

Hi Lana,

The factor (offset) that gets used in the statistical model is actually the *product* of lib.size and norm.factors, so the lower depth of library HCV_100d_2 is taken into account.

Mark

On 2011-05-07, at 9:49 AM, Lana Schaffer wrote:

> Greetings,
> Using d <- calcNormFactors(d)
> I get the following normalization factors.
> Why are the factors so similar when the the 4th count is 1/20 the counts as the rest?
> 
>> d$samples
>           group lib.size norm.factors
> HCV_45d_1    d45  7812615    1.0471701
> HCV_45d_2    d45  9728373    1.0004453
> HCV_100d_1  d100  8606449    0.9516424
> HCV_100d_2  d100   446991    1.0030340
> 
> Lana Schaffer
> Biostatistics, Informatics
> DNA Array Core Facility
> 858-784-2263
> 
> 
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> 
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------------------------------
Mark Robinson, PhD (Melb)
Epigenetics Laboratory, Garvan
Bioinformatics Division, WEHI
e: mrobinson at wehi.edu.au
e: m.robinson at garvan.org.au
p: +61 (0)3 9345 2628
f: +61 (0)3 9347 0852
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