lumi-package problem: nuID [e.g. nuID2EntrezID()] from vignette example throws an error on my system
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Last seen 7.7 years ago
Dear All, I am having trouble running this example code from the lumi-vignette: library(lumi) ## load example data data(example.lumi) if (require(lumiHumanIDMapping)) { nuIDs <- featureNames(example.lumi) mappingInfo <- nuID2EntrezID(nuIDs, lib.mapping=lumiHumanIDMapping) head(mappingInfo) } Then I am seeing this: Error in paste("package", package, sep = ":") : cannot coerce type 'closure' to vector of type 'character' I have come across this problem first when I tried to annotate my own data, but it seems also to happen on my system with every of the nuID mapping commands. Thanks for your help and advise in advance! Best Franzef -- output of sessionInfo(): R version 3.0.3 (2014-03-06) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] de_DE.UTF-8/de_DE.UTF-8/de_DE.UTF-8/C/de_DE.UTF-8/de_DE.UTF-8 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] lumiHumanIDMapping_1.10.0 RSQLite_0.11.4 DBI_0.2-7 [4] AnnotationDbi_1.22.6 lumi_2.12.0 Biobase_2.20.0 [7] BiocGenerics_0.6.0 loaded via a namespace (and not attached): [1] affy_1.38.1 affyio_1.28.0 annotate_1.38.0 beanplot_1.1 [5] BiocInstaller_1.10.2 Biostrings_2.28.0 colorspace_1.2-2 GenomicRanges_1.12.4 [9] grid_3.0.3 illuminaio_0.2.0 IRanges_1.18.1 KernSmooth_2.23-10 [13] lattice_0.20-27 limma_3.16.5 MASS_7.3-29 Matrix_1.1-2 [17] matrixStats_0.8.1 mclust_4.1 methylumi_2.6.1 mgcv_1.7-28 [21] minfi_1.6.0 multtest_2.16.0 nleqslv_2.0 nlme_3.1-113 [25] nor1mix_1.1-4 preprocessCore_1.22.0 R.methodsS3_1.4.2 RColorBrewer_1.0-5 [29] reshape_0.8.4 siggenes_1.34.0 splines_3.0.3 stats4_3.0.3 [33] survival_2.37-7 tools_3.0.3 XML_3.95-0.2 xtable_1.7-1 [37] zlibbioc_1.6.0 -- Sent via the guest posting facility at
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