[BioC] just.gcrma and normalisation
alex lam (RI)
alex.lam at bbsrc.ac.uk
Tue Jun 27 14:33:06 CEST 2006
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?
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