On Mon, Dec 5, 2011 at 12:10 PM, Thomas H. Hampton < Thomas.H.Hampton@dartmouth.edu> wrote: > Hi Sean > > Thanks for the reply. > > I updatred R, biocLite and then lumi. > > Now I am finding lack of mapping library: > > > data <- lumiR("FinalReport.txt", lib = "lumiHumanIDMapping") > Loading required package: lumiHumanIDMapping > Error in addNuID2lumi(x.lumi, lib.mapping = lib.mapping) : > Annotation library lumiHumanIDMapping is not installed! > In addition: Warning message: > In library(package, lib.loc = lib.loc, character.only = TRUE, > logical.return = TRUE, : > there is no package called ‘lumiHumanIDMapping’ > > install.packages("lumiHumanIDMapping") > --- Please select a CRAN mirror for use in this session --- > Loading Tcl/Tk interface ... done > Warning message: > In getDependencies(pkgs, dependencies, available, lib) : > package ‘lumiHumanIDMapping’ is not available (for R version 2.14.0) > > Hi, Tom. You need to use biocLite() to install bioconductor packages. This webpage gives details. http://bioconductor.org/packages/release/data/annotation/html/lumiHuma nIDMapping.html Sean > Wrong library, I guess? > > Tom > > > On Dec 5, 2011, at 9:00 AM, Sean Davis wrote: > > > > 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]]