[BioC] Affymetrix control genes plus links

[Patrícia Luiza Nunes da Costa]

Dear colleagues,

We are trying to analyze a group of Affymetrix arrays, but we don’t have
experience. We performed the RMA normalization and after we analyzed with
the algorithm SOM (3x3 Expander), among others.
We observed that some control genes was differentially expressed in 2/12
arrays (cluster in: http://www.divshare.com/download/4105386-853),
and it shoudn't, isn't it?
The QC stats plot (simpleaffy) seemed good
(http://www.divshare.com/download/4105385-181),
and all parameters indicated by Affymetrix showed results acceptable.

Do you think we have a bug in the experiment?

Should we compare this 2 “different” arrays with the others? Or can we
correct this?

Thanks for your help!

Patricia



Patrícia Luiza Nunes da Costa
Laboratório de Oncologia Experimental, Grupo de Adesão Celular
Faculdade de Medicina da Universidade de Paulo-FM USP
Av. Dr. Arnaldo, 455 sala 4112
Cerqueira Cesar
Cep 01246-903
Tel: (11) 3061-7486 e (11) 8202-7073



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