[BioC] asking with problems with affymetrix data

manzofabio at libero.it manzofabio at libero.it
Fri Oct 3 12:52:30 CEST 2008

Hi everybody,
I'm fabio and I'm trying to analyze some affymetrix data, taken by GEO repository. Series GSE10896. 
I downloaded all the .cel file and with the affy package I read them in R. Then I applied the MAS5 algorthm. The data normilized, I gave a look to the inspective plots (boxplot, MA-plot) and they seem fine. Then I applied the limma to discover differentially expressed genes, but I didn't find anything. The authors applied a wilch test, and so I took the data normilized and I put them in MEV. I applied the wilch test with p.value = 0.05. Then I put them in fold change, but...I didn't find any differences, while the authors 108 genes higher then 1.2. Can someone tell me which mistake I'm doing?

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