[BioC] limma and duplicate correlation

Mark Cowley m.cowley at garvan.org.au
Tue Aug 5 01:06:56 CEST 2008

Hi Yolande,
duplicateCorrelation is designed for the situations where all spots  
are printed 2 or more times, not for handling a small number of probes  
that have been spotted many times.
This is what the help page refers to as "regularly spaced within-array  
replicate spots"

Mark Cowley, BSc (Bioinformatics)(Hons)

Peter Wills Bioinformatics Centre
Garvan Institute of Medical Research, Sydney, Australia

On 05/08/2008, at 3:29 AM, Yolande Tra wrote:

> Dear List,
> I am working on yeast data that has 11 positive controls replicated  
> 17 times. They are irregularly located in the array. After obtaining  
> MA object, I could order the genes and get them next to each other.  
> My question is, how would I incorporate the duplicate correlation  
> aspect when defining the design in limma?
> Thank you for your reply and help.
> Yolande
> 	[[alternative HTML version deleted]]
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