[BioC] limma: duplicates handling

[Jenny Drnevich]

Hi Andres and Jim,

Actually, there is a way that limma accounts for the duplicates and 
only reports one value per clone in topTable. Did you follow the 
Within-Array Replicate Spot example 11.6 in the limmaUsersGuide()? 
After you use duplicateCorrelation() to calculate the correlation 
between spots, you have to modify the call to lmFit:

fit <- lmFit(MA2, design, ndups=2, correlation=corfit$consensus)

Andres - in the future, it would help if you posted your code that 
wasn't working along with the output of sessionInfo() so we could see 
what exactly you did and what you need to do.

Cheers,
Jenny

At 07:59 AM 4/22/2009, James W. MacDonald wrote:
>Hi Andres,
>
>Andres Pinzon wrote:
>>Hi James!
>>On Wed, Apr 22, 2009 at 8:40 AM, James W. MacDonald
>><jmacdon at med.umich.edu> wrote:
>>>Hi Andres,
>>>
>>>Andres Pinzon wrote:
>>>>Hi Everyone,
>>>>
>>>>If I have duplicates in each slide of my experiment, how do I tell limma
>>>>to handle this?
>>>>I am using duplicateCorrelation() function, but after the whole process
>>>>the topTable() reports not half of the spots but all of them,
>>>>For instance, if there are overall 15000 spots in my experiment, and
>>>>half of them are
>>>>duplicates, Shouldn't I end up just with 7500 genes?
>>>Nope. When you use duplicateCorrelation() you are telling limma to fit a
>>>mixed model that accounts for correlation between duplicate spots. But you
>>>are not telling limma to take averages and just report one value.
>>Ok, thanks for answering. Any idea on how to tell limma to take
>>average and report just one value?
>>Sorry I really can not figure it out.
>
>I don't think there are facilities within limma to do this. If this 
>is what you want to do, then you should just compute the averages 
>and then fit the model using the averages.
>
>
>>Best,
>
>--
>James W. MacDonald, M.S.
>Biostatistician
>Douglas Lab
>University of Michigan
>Department of Human Genetics
>5912 Buhl
>1241 E. Catherine St.
>Ann Arbor MI 48109-5618
>734-615-7826
>
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Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
USA

ph: 217-244-7355
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e-mail: drnevich at illinois.edu