Hi everybody! I have been using the oligo package without any problem since a couple of months ago but now when I write the following commands the following error appears when I use the command rma > celFiles<-list.celfiles() > affyRaw<-read.celfiles(celFiles) > ppData<-rma(affyRaw) Error in function (classes, fdef, mtable) : unable to find an inherited method for function ???probeNames??? for signature ???"ExonFeatureSet"??? I have no idea what is happen because last week everything worked properly, any suggestion? Thank you! Maria -- output of sessionInfo(): R version 2.15.3 (2013-03-01) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United Kingdom.1252 [2] LC_CTYPE=English_United Kingdom.1252 [3] LC_MONETARY=English_United Kingdom.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United Kingdom.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] pd.huex.1.0.st.v2_3.8.0 RSQLite_0.11.2 DBI_0.2-5 [4] estrogen_1.8.9 affy_1.36.1 oligo_1.22.0 [7] oligoClasses_1.20.0 PREDA_1.4.0 annotate_1.36.0 [10] AnnotationDbi_1.20.7 multtest_2.14.0 lokern_1.1-3 [13] Biobase_2.18.0 BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] affxparser_1.30.2 affyio_1.26.0 BiocInstaller_1.8.3 [4] Biostrings_2.26.3 bit_1.1-10 codetools_0.2-8 [7] ff_2.2-11 foreach_1.4.0 GenomicRanges_1.10.7 [10] IRanges_1.16.6 iterators_1.0.6 MASS_7.3-23 [13] parallel_2.15.3 preprocessCore_1.20.0 sfsmisc_1.0-23 [16] splines_2.15.3 stats4_2.15.3 survival_2.37-4 [19] tools_2.15.3 XML_3.96-1.1 xtable_1.7-1 [22] zlibbioc_1.4.0 -- Sent via the guest posting facility at bioconductor.org.

Hi Maria, On 4/22/2013 12:36 PM, Maria [guest] wrote: > Hi everybody! > > I have been using the oligo package without any problem since a couple of months ago but now when I write the following commands the following error appears when I use the command rma > >> celFiles<-list.celfiles() >> affyRaw<-read.celfiles(celFiles) >> ppData<-rma(affyRaw) > Error in function (classes, fdef, mtable) : > unable to find an inherited method for function ???probeNames??? for signature ???"ExonFeatureSet"??? > > I have no idea what is happen because last week everything worked properly, any suggestion? It's because you have done something like library(oligo) library(affy) which has caused the rma function in affy to come before the rma function from oligo in the search path. You can either stop loading the affy package, or specify the rma function you want, using the :: accessor: oligo::rma(affyRaw) Best, Jim > > Thank you! > > Maria > > > -- output of sessionInfo(): > > R version 2.15.3 (2013-03-01) > Platform: x86_64-w64-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=English_United Kingdom.1252 > [2] LC_CTYPE=English_United Kingdom.1252 > [3] LC_MONETARY=English_United Kingdom.1252 > [4] LC_NUMERIC=C > [5] LC_TIME=English_United Kingdom.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] pd.huex.1.0.st.v2_3.8.0 RSQLite_0.11.2 DBI_0.2-5 > [4] estrogen_1.8.9 affy_1.36.1 oligo_1.22.0 > [7] oligoClasses_1.20.0 PREDA_1.4.0 annotate_1.36.0 > [10] AnnotationDbi_1.20.7 multtest_2.14.0 lokern_1.1-3 > [13] Biobase_2.18.0 BiocGenerics_0.4.0 > > loaded via a namespace (and not attached): > [1] affxparser_1.30.2 affyio_1.26.0 BiocInstaller_1.8.3 > [4] Biostrings_2.26.3 bit_1.1-10 codetools_0.2-8 > [7] ff_2.2-11 foreach_1.4.0 GenomicRanges_1.10.7 > [10] IRanges_1.16.6 iterators_1.0.6 MASS_7.3-23 > [13] parallel_2.15.3 preprocessCore_1.20.0 sfsmisc_1.0-23 > [16] splines_2.15.3 stats4_2.15.3 survival_2.37-4 > [19] tools_2.15.3 XML_3.96-1.1 xtable_1.7-1 > [22] zlibbioc_1.4.0 > > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099