[BioC] Error while trying to use Genefilter

[Jenny Drnevich]

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] "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
>
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>
>
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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
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ph: 217-244-7355
fax: 217-265-5066
e-mail: drnevich at illinois.edu