[BioC] limma: duplicates handling

[Andres Pinzon]

Hi Jenny,
Thanks for the advice. This is the part of the  code I think is not working:
===
+
+>biolrep <- c(1,1,2,2,3,3)
+>corfit <- duplicateCorrelation(MA,ndups=2,block=biolrep, spacing=8)
+>fit <- lmFit (MA, block=biolrep, cor=corfit$consensus)
+>fit <- eBayes(fit)
+
===

Shoudl I  use something like?:

fit <- lmFit (MA, block=biolrep, ndups=2, spacing=8, cor=corfit$consensus)



best,


On Wed, Apr 22, 2009 at 9:21 AM, Jenny Drnevich <drnevich at illinois.edu> wrote:
> 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
> fax: 217-265-5066
> e-mail: drnevich at illinois.edu
>



-- 
Andrés Pinzón
http://bioinf.ibun.unal.edu.co/~apinzon/
Bioinformatics Center, Colombia EMBnet node
http://bioinf.ibun.unal.edu.co
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Micology and Phytopathology Laboratory - Los Andes University.
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