[BioC] just.gcrma and normalisation

Zhijin (Jean) Wu zwu at alexander.stat.brown.edu
Wed Jun 28 19:10:55 CEST 2006

For a list of normalization methods,
check out the help for function "normalize" in "affy" package. The
available methods can be viewed with "methods(normalize)". There are
invididual help files for each method listed
Here's what I saw:
> methods(normalize)
 [1] normalize.AffyBatch.constant         normalize.AffyBatch.contrasts
 [3] normalize.AffyBatch.invariantset     normalize.AffyBatch.loess
 [5] normalize.AffyBatch.qspline          normalize.AffyBatch.quantiles
 [7] normalize.AffyBatch.quantiles.robust normalize.constant
 [9] normalize.invariantset               normalize.loess
[11] normalize.methods                    normalize.qspline
[13] normalize.quantiles                  normalize.quantiles.robust


On Tue, 27 Jun 2006, alex lam (RI) wrote:

> 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
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