Dear list, I ma still learnig to use the many softwares for gene expression analysis and continue to get an error while trying to filter my eset. Can anyone give me some help on what am I doing wrong? R version 2.8.1 (2008-12-22) Copyright (C) 2008 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. [Previously saved workspace restored] > dir() [1] "Análise affylmGUI" "K562 1.CEL" "K562 2.CEL" [4] "K562 2_1.CEL" "K562 Lucena VCR.txt" "Lucena + VCR 2.CEL" [7] "Lucena + VCR1.CEL" "Lucena sem VCR 1.CEL" "Lucena sem VCR 2.CEL" > library(affy) Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. > Library(tkWidgets) Error: could not find function "Library" > library(tkWidgets) Loading required package: widgetTools Loading required package: tcltk Loading Tcl/Tk interface ... done Loading required package: DynDoc > library(annotate) Loading required package: AnnotationDbi Loading required package: xtable Attaching package: 'xtable' The following object(s) are masked from package:widgetTools : label > library(genefilter) Loading required package: survival Loading required package: splines > library(limma) > library(hgu133a2.db) Loading required package: DBI > data=ReadAffy(widget=True) Error in AllButCelsForReadAffy(..., filenames = filenames, widget = widget, : object "True" not found > data=ReadAffy(widget=TRUE) > library(gcrma) Loading required package: matchprobes > eset=gcrma(data) Adjusting for optical effect....Done. Computing affinities.Done. Adjusting for non-specific binding....Done. Normalizing Calculating Expression > eset.filt = nsFilter(eset, require.entrez=TRUE, remove.dupENTREZ=TRUE, feature.exclude="^AFFX",var.filter=FALSE) Error: getAnnMap: package hgu133plus2 not available Error in mget(featureNames(eset), envir = getAnnEnv(map)) : error in evaluating the argument 'envir' in selecting a method for function 'mget' > eset.filt = nsFilter(eset, require.entrez=TRUE, remove.dupENTREZ=TRUE, feature.exclude="^AFFX",var.filter=FALSE)$eset Error: getAnnMap: package hgu133plus2 not available Error in mget(featureNames(eset), envir = getAnnEnv(map)) : error in evaluating the argument 'envir' in selecting a method for function 'mget' > regards, Marcos B. Pinho Programa de Engenharia Química - PEQ Laboratório de Engenharia de Cultivos Celulares- LECC Universidade Federal do Rio de Janeiro - UFRJ Instituto Nacional de Câncer - INCA Rio de Janeiro - Brasil [[alternative HTML version deleted]]

Hi Marcos, Your arrays are the hgu133plus2, not the hgu133a2, so you need the hgu133plus2.db, not the hgu133a2.db. That's the first problem I noticed, although there might be others. Try this and then see if your code works: source("http://bioconductor.org/biocLite.R") biocLite("hgu133plus2.db") library(hgu133plus2.db) HTH, Jenny P.S. You should update your R version, although if you wait another month or so, an even newer version will be out At 10:49 AM 9/16/2009, Marcos Pinho wrote: >Content-Type: text/plain >Content-Disposition: inline >Content-length: 3285 > >Dear list, > I ma still learnig to use the many softwares for gene expression analysis >and continue to get an error while trying to filter my eset. Can anyone give >me some help on what am I doing wrong? > >R version 2.8.1 (2008-12-22) >Copyright (C) 2008 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. >[Previously saved workspace restored] > > dir() >[1] "An?lise affylmGUI" "K562 1.CEL" "K562 2.CEL" >[4] "K562 2_1.CEL" "K562 Lucena VCR.txt" "Lucena + VCR 2.CEL" >[7] "Lucena + VCR1.CEL" "Lucena sem VCR 1.CEL" "Lucena sem VCR 2.CEL" > > library(affy) >Loading required package: Biobase >Loading required package: tools >Welcome to Bioconductor > Vignettes contain introductory material. To view, type > 'openVignette()'. To cite Bioconductor, see > 'citation("Biobase")' and for packages 'citation(pkgname)'. > > Library(tkWidgets) >Error: could not find function "Library" > > library(tkWidgets) >Loading required package: widgetTools >Loading required package: tcltk >Loading Tcl/Tk interface ... done >Loading required package: DynDoc > > library(annotate) >Loading required package: AnnotationDbi >Loading required package: xtable >Attaching package: 'xtable' > > The following object(s) are masked from package:widgetTools : > label > > library(genefilter) >Loading required package: survival >Loading required package: splines > > library(limma) > > library(hgu133a2.db) >Loading required package: DBI > > data=ReadAffy(widget=True) >Error in AllButCelsForReadAffy(..., filenames = filenames, widget = widget, >: > object "True" not found > > data=ReadAffy(widget=TRUE) > > library(gcrma) >Loading required package: matchprobes > > eset=gcrma(data) >Adjusting for optical effect....Done. >Computing affinities.Done. >Adjusting for non-specific binding....Done. >Normalizing >Calculating Expression > > eset.filt = nsFilter(eset, require.entrez=TRUE, remove.dupENTREZ=TRUE, >feature.exclude="^AFFX",var.filter=FALSE) >Error: getAnnMap: package hgu133plus2 not available >Error in mget(featureNames(eset), envir = getAnnEnv(map)) : > error in evaluating the argument 'envir' in selecting a method for >function 'mget' > > eset.filt = nsFilter(eset, require.entrez=TRUE, remove.dupENTREZ=TRUE, >feature.exclude="^AFFX",var.filter=FALSE)$eset >Error: getAnnMap: package hgu133plus2 not available >Error in mget(featureNames(eset), envir = getAnnEnv(map)) : > error in evaluating the argument 'envir' in selecting a method for >function 'mget' > > > >regards, > >Marcos B. Pinho >Programa de Engenharia Qu?mica - PEQ >Laborat?rio de Engenharia de Cultivos Celulares- LECC >Universidade Federal do Rio de Janeiro - UFRJ >Instituto Nacional de C?ncer - INCA >Rio de Janeiro - Brasil > > [[alternative HTML version deleted]] > > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: >http://news.gmane.org/gmane.science.biology.informatics.conductor Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at illinois.edu