[BioC] Compare subsets using only probesets mapped to chromosome 10

James W. MacDonald jmacdon at med.umich.edu
Tue Aug 19 14:56:27 CEST 2008

Hi Martin,

Martin McCabe wrote:
> Hi.  I've used Affy 133 Plus 2 Arrays on a series of samples and 
> normalised the data using rma.  Can anyone tell me how to run eBayes to 
> compare two subsets of samples (with and without monosomy of chromosome 
> 10) using only probesets mapped to chromosome 10?

I will assume that 'run eBayes' means you want to fit a linear model to 
your data using the limma package.

The eBayes step assumes that you are using all the genes on your chip, 
so you should fit the model up to the eBayes step and then filter on 

To filter on chromosome you can do something like

[Some code to get to this point]
fit2 <- eBayes(fit)
chr10 <- mget("10", revmap(hgu133plus2CHR))[[1]]
just.chr10 <- fit2[chr10,]



> Thanks.
> Dr. Martin G. McCabe
> Cancer Research UK Clinical Research Training Fellow
> Cambridge University Department of Pathology
> Addenbrooke's Hospital
> Cambridge
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James W. MacDonald, M.S.
Hildebrandt Lab
1150 W. Medical Center Drive
Ann Arbor MI 48109-0646

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