[BioC] Basic Question about gcrma & exporting to excel > (command not working)
Dick Beyer
dbeyer at u.washington.edu
Mon Jun 7 17:26:52 CEST 2010
Hi Jennifer,
Check out Jim MacDonald's reply from some time ago:
https://stat.ethz.ch/pipermail/bioconductor/2008-March/021658.html
Cheers,
Dick
*******************************************************************************
Richard P. Beyer, Ph.D. University of Washington
Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695
Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100
Seattle, WA 98105-6099
http://depts.washington.edu/ceeh/members_fc_bioinfo.html
http://staff.washington.edu/~dbeyer
*******************************************************************************
> ------------------------------
>
> Message: 3
> Date: Sun, 06 Jun 2010 21:29:42 -0700
> From: Jennifer Ehren <jehren at salk.edu>
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] Basic Question about gcrma & exporting to excel
> (command not working)
> Message-ID: <4C0C75B6.4020302 at salk.edu>
> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
>
> 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"
>
>
> ------------------------------
>
> Message: 4
> Date: Mon, 7 Jun 2010 10:04:34 +0100
> From: jos matejus <matejus106 at googlemail.com>
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] boxplot error with expression set using oligo package
> and Human gene st 1.0 arrays
> Message-ID:
> <AANLkTinTyNB4X29Mav6YI6Y1-9dujGNVyAixaWlrvUv5 at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Dear All,
>
> I was wondering whether anyone could help decipher an error message I
> am getting when I try to plot a boxplot of normalised expression
> values using the oligo package for human gene st 1.0 arrays. Here is
> the code I am using:
>
> library(oligo)
> library(limma)
> library(genefilter)
> library(pd.hugene.1.0.st.v1)
> library(hugene10sttranscriptcluster.db)
>
> cel.dir <- "C:/cel files"
> cel.files <- list.celfiles(cel.dir, full.names=TRUE)
>
> #construct some phenodata
> theData <- data.frame(Key=rep(c("VitC", "Control"), each=3))
> rownames(theData) <- basename(cel.files)
>
> vMtData <- data.frame(channel = factor("_ALL_",
> levels = c("channel1", "channel2",
> "_ALL_")), labelDescription = "Sample treatment")
>
> pd <- new("AnnotatedDataFrame", data = theData, varMetadata = vMtData)
>
> affyData<-read.celfiles(cel.files, pkgname="pd.hugene.1.0.st.v1", phenoData=pd)
>
> eset <- rma(affyData, target="core")
>
> show(eset)
> #ExpressionSet (storageMode: lockedEnvironment)
> #assayData: 33297 features, 6 samples
> # element names: exprs
> #protocolData: none
> #phenoData
> # rowNames: RB1_A1_140, RB2_A2_14010, ..., RB6_C3_10 ?(6 total)
> #varLabels and varMetadata description:
> # ?Key: Sample treatment
> # ?additional varMetadata: channel
> #featureData: none
> #experimentData: use 'experimentData(object)'
> #Annotation: pd.hugene.1.0.st.v1
>
> boxplot(eset, transfo = identity, main = "After RMA")
>
> #Error in .local(x, ...) : object 'nsamples' not found
>
> I noticed a similar problem was reported in the archives at:
> http://thread.gmane.org/gmane.science.biology.informatics.conductor/29047/focus=29050
>
> however, I am still receiving this error message despite using version
> 1.12.1 of the oligo package. I have also used:
>
> boxplot(exprs(eset))
>
> as suggested by Mike Smith
> (http://thread.gmane.org/gmane.science.biology.informatics.conductor/29047/focus=29050)
>
> but this seems to indicate a large number of outliers which I dont get
> when plotting before normailsation and also when using the
> arrayQualityMetrics package on post processed values.
>
> arrayQualityMetrics(expressionset = eset)
>
> Any help would be gratefully received.
> Best
> Jos
>
> sessionInfo()
> R version 2.11.0 (2010-04-22)
> i386-pc-mingw32
>
> locale:
> [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United
> Kingdom.1252 LC_MONETARY=English_United Kingdom.1252
> [4] LC_NUMERIC=C LC_TIME=English_United
> Kingdom.1252
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] hugene10sttranscriptcluster.db_5.0.1 org.Hs.eg.db_2.4.1
> AnnotationDbi_1.10.1
> [4] pd.hugene.1.0.st.v1_3.0.1 RSQLite_0.9-1
> DBI_0.2-5
> [7] genefilter_1.30.0 limma_3.4.1
> oligo_1.12.1
> [10] oligoClasses_1.10.0 Biobase_2.8.0
>
> loaded via a namespace (and not attached):
> [1] affxparser_1.20.0 affyio_1.16.0 annotate_1.26.0
> Biostrings_2.16.2 IRanges_1.6.4
> [6] preprocessCore_1.10.0 splines_2.11.0 survival_2.35-8
> xtable_1.5-6
>
>
>
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> End of Bioconductor Digest, Vol 88, Issue 7
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