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/window s/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 > > > > ------------------------------ > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > End of Bioconductor Digest, Vol 88, Issue 7 > ******************************************* >