[BioC] Basic Question about gcrma & exporting to excel (command not working)
jehren at salk.edu
Mon Jun 7 06:29:42 CEST 2010
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
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:
> setwd("C:\\affy\\Jennifer") normalized<-justGCRMA()
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
_*SESSION OUTPUT INFORMATION
*_R version 2.10.1 (2009-12-14)
Copyright (C) 2009 The R Foundation for Statistical Computing
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
Using R version 2.10.1, biocinstall version 2.5.10.
Installing Bioconductor version 2.5 packages:
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)
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
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)'.
Computing affinitiesLoading required package: AnnotationDbi
Adjusting for optical effect.......Done.
Adjusting for non-specific binding......Done.
Error: could not find function "exprs2excel"
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