Hi Christian,
That's VERY interesting.
I've observed identical expression levels across probesets in newer ST  
arrays, (& now that the authors mention it, probably more frequently  
with odd numbers of arrays), but I can't say i've ever noticed the  
phenomena in the older 3' arrays.

Does your implementation of tRMA also apply to oligo/ST arrays?

cheers,
Mark

On 03/12/2010, at 8:17 AM, cstrato wrote:

> Dear All,
>
> Recently I found an interesting paper about problems with RMA when  
> applied to small sample sets which are based on the median-polish  
> algorithm, see:
> http://www.biomedcentral.com/1471-2105/11/553/abstract
>
> Since the authors offer a simple solution to the problem I thought  
> it might be of interest to users that I have implemented function  
> "trma()" in the development version "xps_1.11.3".
>
> Best regards
> Christian
> _._._._._._._._._._._._._._._._._._
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-----------------------------------------------------
Mark Cowley, PhD

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


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