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?

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[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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