Entering edit mode
Jennifer Ehren
▴
10
@jennifer-ehren-4115
Last seen 10.6 years ago
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:
|write.table|
write.csv(normalized,file="NormalGCRMA.csv")
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
ISBN 3-900051-07-0
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.
> 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
.Done.
Adjusting for optical effect.......Done.
Adjusting for non-specific binding......Done.
Normalizing
Calculating Expression
> exprs2excel(normalized,file="NormalGCRMA.csv")
Error: could not find function "exprs2excel"
