[BioC] calcNormFactors - normalization

[Lana Schaffer]

Mark,
Thanks.
Can you use this package for only 1 sample each group?
Lana

-----Original Message-----
From: Mark Robinson [mailto:mrobinson at wehi.EDU.AU] 
Sent: Friday, May 06, 2011 5:15 PM
To: Lana Schaffer
Cc: 'bioconductor at r-project.org'
Subject: Re: [BioC] calcNormFactors - normalization


On 2011-05-07, at 9:57 AM, Lana Schaffer wrote:

> Mark,
> My gene library contains only 141 genes.  Is this low number
> Alright in this model?

Yes, this is alright.  For one thing, you pay a much smaller multiple testing penalty.

> The length on the genes are not accounted for in this package edgeR?

Correct, not accounted for.  But, you are comparing genes across samples.

Mark


> 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
>> 
>> 
>> 	[[alternative HTML version deleted]]
>> 
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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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