[BioC] calcNormFactors - normalization

[Lana Schaffer]

Davis,
Untranslated this means that the package doesn't handle just 1 sample per group,
For both groups.
Lana

-----Original Message-----
From: Davis McCarthy [mailto:dmccarthy at wehi.EDU.AU] 
Sent: Saturday, May 07, 2011 12:41 AM
To: Lana Schaffer
Cc: 'Mark Robinson'; 'bioconductor at r-project.org'
Subject: Re: [BioC] calcNormFactors - normalization

Hi Lana

The package can handle more than one sample per group and indeed the full
utility of the methods in edgeR are unlocked when there is replication in
at least one group.

Cheers
Davis


> 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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--------------------------------------------------
Davis J McCarthy
Research Technician
Bioinformatics Division
Walter and Eliza Hall Institute of Medical Research
1G Royal Parade, Parkville, Vic 3052, Australia.
dmccarthy at wehi.edu.au
http://www.wehi.edu.au


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