[BioC] Should I compute RMA expression measures separately for different treament groups?

[Clémentine Dressaire]

 Dear BioC users,

 I was wondering wether it would not make sense to perform rma 
 normalization on the 2 (or more) conditions we want to compare 
 separately instead of alltogether as usually performed.
 This questioning comes from the three conditions I currently have to 
 deal with. They clearly display different raw levels and I'm afraid that 
 using global RMA will somehow hide an effect that could be meaningful. 
 To illustrate I put in attachement the boxplots obtained before and 
 after the two "types" of rma normalization.

 Did anyone already have to deal with such a problem? Do you have any 
 suggestions?

 Many thanks for your help,

 Clémentine

-- 
 Clémentine Dressaire
 Post-doctoral research fellow
 Control of gene expression lab
 ITQB - Instituto de Tecnologia Química e Biológica
 Apartado 127, Av. da República
 2780-157 Oeiras
 Portugal
 +351 214469562