[BioC] Basic Question about gcrma & exporting to excel (command not working)

Jennifer Ehren jehren at salk.edu
Mon Jun 7 06:29:42 CEST 2010

Hi List,

I am relatively new to Bioconductor and microarray data analysis.  I apologize for the simple question, but when
I performed a search for the answer to my question, I could not find it in the archive (probably because my question is
so basic). 

Sorry if I offend with my trivial question.

I am trying to normalize Affy microarray data.  A former colleague of mine has an old version of R (R Gui?) and would 
run the following commands.  It works fine for him, but I don't have access to his version of R.  I have R 
version 2.10.1 and the command to export to excel won't work.  I receive the error message:  
Error: could not find function "exprs2excel".  Is there a way to rectify my problem/an alternative command I can use?
Perhaps the command has been modified with the newer version of R?

My R Script is as follows:
> library(gcrma)
> setwd("C:\\affy\\Jennifer") normalized<-justGCRMA()
> exprs2excel(normalized,file="NormalGCRMA.csv")

Below is a copy of the output of the session information.

The following commands don't output what I need either: 

I'm sure I'm doing something silly, but I'm stuck right now and currently, no one in my lab uses R.

Thanks in advance,  Jennifer

*_R version 2.10.1 (2009-12-14)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

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You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

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> source("http://bioconductor.org/biocLite.R")
> biocLite("gcrma")
Using R version 2.10.1, biocinstall version 2.5.10.
Installing Bioconductor version 2.5 packages:
[1] "gcrma"
Please wait...

trying URL 'http://www.bioconductor.org/packages/2.5/bioc/bin/windows/contrib/2.10/gcrma_2.18.1.zip'
Content type 'application/zip' length 162231 bytes (158 Kb)
opened URL
downloaded 158 Kb

package 'gcrma' successfully unpacked and MD5 sums checked

The downloaded packages are in
        C:\Documents and Settings\CNB User\Local Settings\Temp\RtmpOxm0WC\downloaded_packages
> library(gcrma)
Loading required package: affy
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

> setwd("C:\\affy\\Jennifer")
> normalized<-justGCRMA()
Computing affinitiesLoading required package: AnnotationDbi
Adjusting for optical effect.......Done.
Adjusting for non-specific binding......Done.
Calculating Expression
> exprs2excel(normalized,file="NormalGCRMA.csv")
Error: could not find function "exprs2excel"

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