Dear R-B Experts, I ran into a problem using the oligo package to analyze mgst arrays. It seems the read.celfiles() did not actually read in the new data but instead keeping the old data read in previously. > library(oligo) > library(pd.mogene.1.0.st.v1) > geneCELs <- list.celfiles("/Data_Analysis/Yu2011_183mgst", full.names = TRUE) > affyGenesFS <- read.celfiles (geneCELs) Platform design info loaded. Reading in : /Data_Analysis/Yu2011_183mgst/2011-183_MUT1_(MoGene- 1_0-st-v1).CEL Reading in : /Data_Analysis/Yu2011_183mgst/2011-183_MUT2_(MoGene- 1_0-st-v1).CEL Reading in : /Data_Analysis/Yu2011_183mgst/2011-183_MUT3_(MoGene- 1_0-st-v1).CEL Reading in : /Data_Analysis/Yu2011_183mgst/2011-183_WT1_(MoGene- 1_0-st-v1).CEL Reading in : /Data_Analysis/Yu2011_183mgst/2011-183_WT2_(MoGene- 1_0-st-v1).CEL Reading in : /Data_Analysis/Yu2011_183mgst/2011-183_WT3_(MoGene- 1_0-st-v1).CEL > affyGeneFS GeneFeatureSet (storageMode: lockedEnvironment) assayData: 1102500 features, 33 samples element names: exprs protocolData rowNames: TisMap_Brain_01_v1_WTGene1.CEL TisMap_Brain_02_v1_WTGene1.CEL ... TisMap_Thyroid_03_v1_WTGene1.CEL (33 total) varLabels: exprs dates varMetadata: labelDescription channel phenoData rowNames: TisMap_Brain_01_v1_WTGene1.CEL TisMap_Brain_02_v1_WTGene1.CEL ... TisMap_Thyroid_03_v1_WTGene1.CEL (33 total) varLabels: index varMetadata: labelDescription channel featureData: none experimentData: use 'experimentData(object)' Annotation: pd.hugene.1.0.st.v1 This remains the same even after I reload all the packages again and started fresh. Any help would be greatly appreciated. Here is the session info: > sessionInfo() R version 2.12.2 (2011-02-25) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] pd.hugene.1.0.st.v1_3.0.2 oligoData_1.0.0 pd.mogene.1.0.st.v1_3.0.2 oligo_1.14.0 oligoClasses_1.12.2 [6] RColorBrewer_1.0-2 geneplotter_1.28.0 annotate_1.28.1 annaffy_1.22.0 KEGG.db_2.4.5 [11] GO.db_2.4.5 RSQLite_0.9-3 DBI_0.2-5 AnnotationDbi_1.12.0 affyQCReport_1.28.1 [16] lattice_0.19-13 simpleaffy_2.26.1 genefilter_1.32.0 limma_3.6.9 affyPLM_1.26.1 [21] preprocessCore_1.12.0 gcrma_2.22.0 affydata_1.11.11 affy_1.28.0 Biobase_2.10.0 [26] R.utils_1.5.7 R.oo_1.7.4 R.methodsS3_1.2.1 loaded via a namespace (and not attached): [1] affxparser_1.22.1 affyio_1.18.0 Biostrings_2.18.4 grid_2.12.2 IRanges_1.8.9 splines_2.12.2 survival_2.36-1 tools_2.12.2 [9] xtable_1.5-6 Best, Yongde

the name of the object where you read your files into is: affyGenesFS and not affyGeneFS b On 24 May 2011 23:32, YBao <yb8d at="" virginia.edu=""> wrote: > Dear R-B Experts, > > I ran into a problem using the oligo package to analyze mgst arrays. > It seems the read.celfiles() did not actually read in the new data but > instead keeping the old data read in previously. >> library(oligo) >> library(pd.mogene.1.0.st.v1) >> geneCELs <- list.celfiles("/Data_Analysis/Yu2011_183mgst", full.names = TRUE) >> affyGenesFS <- read.celfiles (geneCELs) > Platform design info loaded. > Reading in : /Data_Analysis/Yu2011_183mgst/2011-183_MUT1_(MoGene- 1_0-st-v1).CEL > Reading in : /Data_Analysis/Yu2011_183mgst/2011-183_MUT2_(MoGene- 1_0-st-v1).CEL > Reading in : /Data_Analysis/Yu2011_183mgst/2011-183_MUT3_(MoGene- 1_0-st-v1).CEL > Reading in : /Data_Analysis/Yu2011_183mgst/2011-183_WT1_(MoGene- 1_0-st-v1).CEL > Reading in : /Data_Analysis/Yu2011_183mgst/2011-183_WT2_(MoGene- 1_0-st-v1).CEL > Reading in : /Data_Analysis/Yu2011_183mgst/2011-183_WT3_(MoGene- 1_0-st-v1).CEL >> affyGeneFS > GeneFeatureSet (storageMode: lockedEnvironment) > assayData: 1102500 features, 33 samples > ?element names: exprs > protocolData > ?rowNames: TisMap_Brain_01_v1_WTGene1.CEL > TisMap_Brain_02_v1_WTGene1.CEL ... TisMap_Thyroid_03_v1_WTGene1.CEL > (33 total) > ?varLabels: exprs dates > ?varMetadata: labelDescription channel > phenoData > ?rowNames: TisMap_Brain_01_v1_WTGene1.CEL > TisMap_Brain_02_v1_WTGene1.CEL ... TisMap_Thyroid_03_v1_WTGene1.CEL > (33 total) > ?varLabels: index > ?varMetadata: labelDescription channel > featureData: none > experimentData: use 'experimentData(object)' > Annotation: pd.hugene.1.0.st.v1 > > This remains the same even after I reload all the packages again and > started fresh. Any help would be greatly appreciated. > > Here is the session info: >> sessionInfo() > R version 2.12.2 (2011-02-25) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base > > other attached packages: > ?[1] pd.hugene.1.0.st.v1_3.0.2 oligoData_1.0.0 > pd.mogene.1.0.st.v1_3.0.2 oligo_1.14.0 > oligoClasses_1.12.2 > ?[6] RColorBrewer_1.0-2 ? ? ? ?geneplotter_1.28.0 > annotate_1.28.1 ? ? ? ? ? annaffy_1.22.0 ? ? ? ? ? ?KEGG.db_2.4.5 > [11] GO.db_2.4.5 ? ? ? ? ? ? ? RSQLite_0.9-3 ? ? ? ? ? ? DBI_0.2-5 > ? ? ? ? ? ?AnnotationDbi_1.12.0 ? ? ?affyQCReport_1.28.1 > [16] lattice_0.19-13 ? ? ? ? ? simpleaffy_2.26.1 > genefilter_1.32.0 ? ? ? ? limma_3.6.9 ? ? ? ? ? ? ? affyPLM_1.26.1 > [21] preprocessCore_1.12.0 ? ? gcrma_2.22.0 > affydata_1.11.11 ? ? ? ? ?affy_1.28.0 ? ? ? ? ? ? ? Biobase_2.10.0 > [26] R.utils_1.5.7 ? ? ? ? ? ? R.oo_1.7.4 > R.methodsS3_1.2.1 > > loaded via a namespace (and not attached): > [1] affxparser_1.22.1 affyio_1.18.0 ? ? Biostrings_2.18.4 grid_2.12.2 > ? ? IRanges_1.8.9 ? ? splines_2.12.2 ? ?survival_2.36-1 > tools_2.12.2 > [9] xtable_1.5-6 > > Best, > > Yongde > > _______________________________________________ > 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 > -- Successful people ask better questions, and as a result, they get better answers. (Tony Robbins)