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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