Hi Pedro,

without knowing details (or anything about global repression in  
yeast), I would guess that your problem is normalization. Both MAS5  
and (GC)RMA normalization assume that you have basically the same  
distribution of expression values on each chip, if you look across  
all the probes/probe-sets on each chip. It sounds as if in your  
study, that is not the case; both normalization schemes are likely to  
break down, and they will do so in different manners.

In your situation, I'd probably look at the actual distribution of  
probes/probe-sets first to get an impression what goes wrong. Then  
I'd try to find out what people using boutique chips (with less than  
say a thousand clones/probes) have been doing, as they should face a  
similar problem.

Regards,

alexander

On 3 Apr 2006, at 10:51, Pedro Botías wrote:

> Dear all,
> We are studying the changes on yeast gene expression under  
> conditions that lead to extreme changes in the transcriptome (we  
> think to global repression) and finally to cell death. We are using  
> Affymetrix technology and finding a great discrepancy between MAS  
> and GCRMA analysis, much more than in other studies with less  
> transcriptional changes.
> Does anybody work with data in a situation of global severe  
> repression? From these two analysis, what could fit better to our  
> experimental conditions?
> Thanks for your help.
>
> Pedro Botías Talamantes
> Unidad de Genómica
> Parque Científico de Madrid-UCM
> Facultad CC Biológicas- Planta sótano
> Universidad Complutense de Madrid
> 28040 Madrid
>
> Tel: 91 3945036
> FAX 91 3944883
> e-mail: pbotias@bio.ucm.es
> Web: http://www.ucm.es/info/gyp/genomica/
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>
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Alexander.Ploner@ki.se
Medical Epidemiology & Biostatistics
Karolinska Institutet, Stockholm
Tel: ++46-8-524-82329
Fax: ++46-8-31 49 75



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