[BioC] Correlation analysis of replicates

[Mark Cowley]

Hi Kai,
i'm not sure about your first question, but...
re the correlation coefficient, take a look at the GeneSelector  
package. In their original paper, they called  the correlation an  
OrderScore if I recall correctly.
cheers,
Mark
-----------------------------------------------------
Mark Cowley, PhD

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

On 06/11/2009, at 5:37 AM, K Tre wrote:

> Hi,
>
> We are trying to compare affymetrix genelists generated a while back
> using MAS 5.0 to the new genelists generated using RMA analysis.
> Previously, we used to perform a comparison expression analysis of the
> replicates first (3 replicates for each condition) in order to  
> determine the
> false positive rate. Is there a way to do something similar in RMA  
> just for
> comparative purposes?
> Also, is it possible to compare only 2 chips at a time and generate a
> correlation coefficient? I checked the posting guide but couldn't  
> find a
> previous email that would answer this question.
>
> Any help or pointing where to look is much appreciated,
> Thanks,
> Kai
>
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>
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