[BioC] just.gcrma and normalisation

alex lam (RI) alex.lam at bbsrc.ac.uk
Tue Jun 27 14:33:06 CEST 2006

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? 


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

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

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