[BioC] RMA results

[Oliver Hartmann]

Take a look at my poster
Comparison of Normalization Methods and Signal Intensity Measures for 
Affymetrix GeneChips(R).

at http://staff-www.uni-marburg.de/~hartmann/

and you will see why you got 10-fold expression with Affy MAS and not 
with rma()... it's an ilustration of Rafael answered you already...

> Date: Wed, 22 Jan 2003 08:33:02 -0500
> From: "Duhaime Johanne" <Johanne.Duhaime@ircm.qc.ca>
> To: <bioconductor@stat.math.ethz.ch>
> Subject: [BioC] RMA results
> 
> 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


-- 
Oliver Hartmann, Institute of Medical Biometry and Epidemiology
Philipps-University Marburg, Bunsenstr. 3, D-35037 Marburg
phone +49(0)6421 28 66514, fax +49(0)6421 28 68921