[BioC] RMA results

[Duhaime Johanne]

Hello

We are using the last version (version 1.1) for windows. We just start to use the software.
We had previously analysed our data with Affymetrix and GeneSpring. 

We used RMA method (rma()) to normalize and calculate the expression value of 5 version mgu74 (not V2) affy chips.
We had some genes that had 5 to 10 fold change with Affy and GeneSpring. Now we got everything around 1 as  fold change with rma. 
Is someone can explain me this result?

Thank you in advance

Johanne Duhaime
IRCM
duhaimj@ircm.qc.ca
tel: (514) 987-5556
fax: (514) 987-5644
www.ircm.qc.ca