[BioC] missing functions in affy package

Henrik Bengtsson hb at stat.berkeley.edu
Mon Nov 3 23:20:28 CET 2008

There is definitely a normalize.quantiles() in the preprocessCore package:

> str(preprocessCore::normalize.quantiles)
function (x, copy = TRUE)

> packageDescription("preprocessCore");

Package: preprocessCore
Version: 1.3.4
Title: A collection of pre-processing functions
Author: Benjamin Milo Bolstad <bmb at bmbolstad.com>
Maintainer: Benjamin Milo Bolstad <bmb at bmbolstad.com>
Depends: methods
Description: A library of core preprocessing routines
License: LGPL version 2 or newer
Collate: normalize.quantiles.R quantile_extensions.R
        rma.background.correct.R rcModel.R colSummarize.R
        subColSummarize.R plmr.R plmd.R init.R
LazyLoad: yes
biocViews: Infrastructure
Packaged: Sat Aug 2 15:26:12 2008; biocbuild
Built: R 2.8.0; i386-pc-mingw32; 2008-08-02 21:09:33; windows

Please report you sessionInfo() etc when you post questions/comments like this.


On Mon, Nov 3, 2008 at 12:16 PM, Rachael Hageman
<Rachael.Hageman at jax.org> wrote:
> To Whom it May Concern,
> I use the function "normalize.quantiles" in the preprocessCore/affy package on a regular basis for my illumina data.  I have recently installed the latest version of R (2.8) and the affy package off of Bioconductor.  I noticed that this function no longer exists within the package.  I wonder if this is an oversight on my part, or if it isn't, is there is a reason it was pulled from the package?  I am on a Mac, although my Windows machine has the same problem with the new version.
> Thanks in advance,
> Rachael
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