[BioC] limma: duplicates handling

James W. MacDonald jmacdon at med.umich.edu
Wed Apr 22 14:59:15 CEST 2009

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.
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618

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