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

[Benilton Carvalho]

instead of exprs2excel(), use write.exprs()

b

On 7 June 2010 05:29, Jennifer Ehren <jehren at salk.edu> wrote:
> 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"
>
>
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