[BioC] just.gcrma and normalisation

[alex lam (RI)]

Dear colleagues,

I am very new to this so please forgive me if this question is too
basic. I couldn't find an answer in the archive.

I am trying to pre-process a large number of affy arrays and use the
expression values in a linkage analysis for expression QTL mapping. I
ran just.gcrma on the data because running ReadAffy then gcrma didn't
work on so many arrays. It returned an exprSet object which has been
normalised. But I have a feeling that the default quantile normalisation
is not suitable for what I want to do.

I think I can turn normalisation off, but then how do I apply other
types of normalisation on an exprSet object? Expresso can only take an
AffyBatch object, right? 

Cheers,
Alex

------------------------------------
Alex Lam
PhD student
Department of Genetics and Genomics
Roslin Institute (Edinburgh)
Roslin
Midlothian EH25 9PS

Phone +44 131 5274471
Web   http://www.roslin.ac.uk