[BioC] limma: duplicates handling

[Andres Pinzon]

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.

Best,

-- 
Andrés Pinzón
http://bioinf.ibun.unal.edu.co/~apinzon/
Bioinformatics Center, Colombia EMBnet node
http://bioinf.ibun.unal.edu.co
Tel +57 3165000 ext 16961 Fax +571 3165415
Micology and Phytopathology Laboratory - Los Andes University.
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Tel +571 3394949 ext. 2768