help with Starr
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Yongde Bao ▴ 170
@yongde-bao-244
Last seen 7.1 years ago
Dear BioConductors, While trying to go over the demo data in the package Starr, I encountered this error message: > dataPath <- system.file("extdata", package = "Starr") > bpmapChr1 <- readBpmap(file.path(dataPath, "Scerevisiae_tlg_chr1.bpmap")) > cels <- c(file.path(dataPath, "Rpb3_IP_chr1.cel"), file.path(dataPath, "wt_IP_chr1.cel"), file.path(dataPath, "Rpb3_IP2_chr1.cel")) > names <- c("rpb3_1", "wt_1", "rpb3_2") > type <- c("IP", "CONTROL", "IP") > rpb3Chr1 <- readCelFile(bpmapChr1, cels, names, type, featureData = T, log.it = T) Error: could not find function "readCelFile" > 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] grid stats graphics grDevices utils datasets methods base other attached packages: [1] affxparser_1.22.1 affy_1.28.0 Ringo_1.14.0 Matrix_0.999375-46 lattice_0.19-13 limma_3.6.9 RColorBrewer_1.0-2 Biobase_2.10.0 [9] R.utils_1.5.7 R.oo_1.7.4 R.methodsS3_1.2.1 loaded via a namespace (and not attached): [1] affyio_1.18.0 annotate_1.28.1 AnnotationDbi_1.12.0 DBI_0.2-5 genefilter_1.32.0 preprocessCore_1.12.0 RSQLite_0.9-3 [8] splines_2.12.2 survival_2.36-1 tools_2.12.2 xtable_1.5-6 Any help? Can it be an issue of R version so the Starr should be used in in R Devel? Best, Yongde
GO Starr GO Starr • 593 views
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@martin-morgan-1513
Last seen 3 months ago
United States
On 05/30/2011 07:10 AM, YBao wrote: > Dear BioConductors, > > While trying to go over the demo data in the package Starr, I > encountered this error message: > >> dataPath<- system.file("extdata", package = "Starr") >> bpmapChr1<- readBpmap(file.path(dataPath, "Scerevisiae_tlg_chr1.bpmap")) >> cels<- c(file.path(dataPath, "Rpb3_IP_chr1.cel"), file.path(dataPath, "wt_IP_chr1.cel"), file.path(dataPath, "Rpb3_IP2_chr1.cel")) >> names<- c("rpb3_1", "wt_1", "rpb3_2") >> type<- c("IP", "CONTROL", "IP") >> rpb3Chr1<- readCelFile(bpmapChr1, cels, names, type, featureData = T, log.it = T) > Error: could not find function "readCelFile" > >> 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] grid stats graphics grDevices utils datasets > methods base > > other attached packages: > [1] affxparser_1.22.1 affy_1.28.0 Ringo_1.14.0 > Matrix_0.999375-46 lattice_0.19-13 limma_3.6.9 > RColorBrewer_1.0-2 Biobase_2.10.0 > [9] R.utils_1.5.7 R.oo_1.7.4 R.methodsS3_1.2.1 > > loaded via a namespace (and not attached): > [1] affyio_1.18.0 annotate_1.28.1 AnnotationDbi_1.12.0 > DBI_0.2-5 genefilter_1.32.0 preprocessCore_1.12.0 > RSQLite_0.9-3 > [8] splines_2.12.2 survival_2.36-1 tools_2.12.2 > xtable_1.5-6 > > Any help? Can it be an issue of R version so the Starr should be used > in in R Devel? Hi Yongde -- 'Starr' is not listed as 'other attached packages' so I think you're missing a library(Starr) The usual advice is to use a current R (2.13) and associated Bioconductor packages. Martin > > 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 -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793
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