My attempt to create a lumi batch fails when I use a final report text file as input. The text file has the following columns: [1] "TargetID" "ProbeID" [3] "X6303230026_A.AVG_Signal" "X6303230026_A.Detection.Pval" [5] "X6303230026_B.AVG_Signal" "X6303230026_B.Detection.Pval" [7] "X6303230026_C.AVG_Signal" "X6303230026_C.Detection.Pval" [9] "X6303230026_D.AVG_Signal" "X6303230026_D.Detection.Pval" [11] "X6303230026_E.AVG_Signal" "X6303230026_E.Detection.Pval" [13] "X6303230026_F.AVG_Signal" "X6303230026_F.Detection.Pval" [15] "X6303230026_G.AVG_Signal" "X6303230026_G.Detection.Pval" [17] "X6303230026_H.AVG_Signal" "X6303230026_H.Detection.Pval" [19] "X6303230026_I.AVG_Signal" "X6303230026_I.Detection.Pval" [21] "X6303230026_J.AVG_Signal" "X6303230026_J.Detection.Pval" [23] "X6303230026_K.AVG_Signal" "X6303230026_K.Detection.Pval" [25] "X6303230026_L.AVG_Signal" "X6303230026_L.Detection.Pval" [27] "SEARCH_KEY" "ACCESSION" [29] "SYMBOL" "PROBE_ID" [31] "PROBE_START" "CHROMOSOME" [33] "PROBE_CHR_ORIENTATION" "PROBE_COORDINATES" [35] "DEFINITION" I am using the following command to read the data in: data <- lumiR("FinalReport.txt", lib = "lumiHumanIDMapping") which finished without error. > data ExpressionSet (storageMode: lockedEnvironment) assayData: 47231 features, 12 samples element names: detection, exprs protocolData: none phenoData sampleNames: 6303230026_A 6303230026_B ... 6303230026_L (12 total) varLabels: sampleID varMetadata: labelDescription featureData featureNames: Ku8QhfS0n_hIOABXuE fqPEquJRRlSVSfL.8A ... N8t5EuJCr0Tk9.zHno (47231 total) fvarLabels: ProbeID TargetID ... DEFINITION (9 total) fvarMetadata: labelDescription experimentData: use 'experimentData(object)' Annotation: lumiHumanAll.db As I understand it, "data" above should be a lumi batch. > sessionInfo() R version 2.12.0 (2010-10-15) Platform: i386-apple-darwin9.8.0/i386 (32-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] limma_3.6.9 lumiHumanAll.db_1.12.0 org.Hs.eg.db_2.4.6 [4] annotate_1.28.0 lumiHumanIDMapping_1.8.0 RSQLite_0.9-4 [7] DBI_0.2-5 AnnotationDbi_1.12.0 lumi_2.2.1 [10] Biobase_2.10.0 loaded via a namespace (and not attached): [1] affy_1.28.0 affyio_1.18.0 grid_2.12.0 [4] hdrcde_2.15 KernSmooth_2.23-6 lattice_0.19-33 [7] MASS_7.3-11 Matrix_0.999375-50 methylumi_1.6.1 [10] mgcv_1.7-6 nlme_3.1-98 preprocessCore_1.12.0 [13] tools_2.12.0 xtable_1.5-6 Best, Tom [[alternative HTML version deleted]]

On Mon, Dec 5, 2011 at 8:48 AM, Thomas H. Hampton < Thomas.H.Hampton@dartmouth.edu> wrote: > My attempt to create a lumi batch fails when I use a final report text > file as input. > > The text file has the following columns: > > [1] "TargetID" "ProbeID" > [3] "X6303230026_A.AVG_Signal" "X6303230026_A.Detection.Pval" > [5] "X6303230026_B.AVG_Signal" "X6303230026_B.Detection.Pval" > [7] "X6303230026_C.AVG_Signal" "X6303230026_C.Detection.Pval" > [9] "X6303230026_D.AVG_Signal" "X6303230026_D.Detection.Pval" > [11] "X6303230026_E.AVG_Signal" "X6303230026_E.Detection.Pval" > [13] "X6303230026_F.AVG_Signal" "X6303230026_F.Detection.Pval" > [15] "X6303230026_G.AVG_Signal" "X6303230026_G.Detection.Pval" > [17] "X6303230026_H.AVG_Signal" "X6303230026_H.Detection.Pval" > [19] "X6303230026_I.AVG_Signal" "X6303230026_I.Detection.Pval" > [21] "X6303230026_J.AVG_Signal" "X6303230026_J.Detection.Pval" > [23] "X6303230026_K.AVG_Signal" "X6303230026_K.Detection.Pval" > [25] "X6303230026_L.AVG_Signal" "X6303230026_L.Detection.Pval" > [27] "SEARCH_KEY" "ACCESSION" > [29] "SYMBOL" "PROBE_ID" > [31] "PROBE_START" "CHROMOSOME" > [33] "PROBE_CHR_ORIENTATION" "PROBE_COORDINATES" > [35] "DEFINITION" > > I am using the following command to read the data in: > > data <- lumiR("FinalReport.txt", lib = "lumiHumanIDMapping") > > which finished without error. > > > data > ExpressionSet (storageMode: lockedEnvironment) > assayData: 47231 features, 12 samples > element names: detection, exprs > protocolData: none > phenoData > sampleNames: 6303230026_A 6303230026_B ... 6303230026_L (12 total) > varLabels: sampleID > varMetadata: labelDescription > featureData > featureNames: Ku8QhfS0n_hIOABXuE fqPEquJRRlSVSfL.8A ... > N8t5EuJCr0Tk9.zHno (47231 total) > fvarLabels: ProbeID TargetID ... DEFINITION (9 total) > fvarMetadata: labelDescription > experimentData: use 'experimentData(object)' > Annotation: lumiHumanAll.db > > As I understand it, "data" above should be a lumi batch. > > > sessionInfo() > R version 2.12.0 (2010-10-15) > Platform: i386-apple-darwin9.8.0/i386 (32-bit) > > Hi, Tom. I think you might need to update your R and bioconductor. I don't know what the behavior for lumiR was a couple of versions of R ago, but I believe the current version returns a lumiBatch. Sean > 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] limma_3.6.9 lumiHumanAll.db_1.12.0 org.Hs.eg.db_2.4.6 > [4] annotate_1.28.0 lumiHumanIDMapping_1.8.0 RSQLite_0.9-4 > [7] DBI_0.2-5 AnnotationDbi_1.12.0 lumi_2.2.1 > [10] Biobase_2.10.0 > > loaded via a namespace (and not attached): > [1] affy_1.28.0 affyio_1.18.0 grid_2.12.0 > [4] hdrcde_2.15 KernSmooth_2.23-6 lattice_0.19-33 > [7] MASS_7.3-11 Matrix_0.999375-50 methylumi_1.6.1 > [10] mgcv_1.7-6 nlme_3.1-98 preprocessCore_1.12.0 > [13] tools_2.12.0 xtable_1.5-6 > > Best, > > Tom > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]