[BioC] Quantile normalization without using affyBatch
gopalans at comcast.net
Tue Apr 19 20:07:44 CEST 2005
normalize.quantiles(matrixofvalues) should work.
(Suresh Gopalan, PhD)
----- Original Message -----
From: "Shinhan Shiu" <shiu at uchicago.edu>
To: <bioconductor at stat.math.ethz.ch>
Sent: Tuesday, April 19, 2005 12:52 PM
Subject: [BioC] Quantile normalization without using affyBatch
>I am working on Arabidopsis tiling array data. I want to adjust the
>intensity based on GC content then do normalization. But the CDF and CEL
>files are not available so the sequences and raw intensities are downloaded
>from Gene Expression Omnibus instead.
> I have extracted codes from gcrma and the hacked version works fine for
> background correction and affinity adjustment. I run into trouble,
> however, when I try to do quantile normalization.
> The method "normalize" takes an affyBatch object but I am working with a
> matrix of numbers. I wonder if there is any work around or other methods I
> can use.
> Shinhan Shiu
> Dept. of Ecology and Evolution
> University of Chicago
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
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