[BioC] limma: duplicates handling

James W. MacDonald jmacdon at med.umich.edu
Wed Apr 22 14:40:34 CEST 2009

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.



> Thank you for your time.
> 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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