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Question: Error in package goseq
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gravatar for Joydeep Mitra
8.3 years ago by
Joydeep Mitra10 wrote:
Hi, I am a grad student at Institute of Bioinformatics, University of Georgia, USA. I have been trying to use the bioconductor package goseq for go- term/pathway enrichment of my expression data. Since my organism of interest isn't included in the goseq database, I am manually entering the data for gene lengths and categories following the directions in the vignette provided with the package. I have tried representing the gene-category mappings in both data frame and list formats as specified. While the 'nullp' function worked fine for my data, when I run goseq() with the following command, I get an error message: > eco1.gs<-goseq(DEgenes=eco1.de,pwf=eco1.pwf,gene2cat=ids.go.list) Using manually entered categories. Error in summary(map)[, 1] : incorrect number of dimensions Here's my session info: > sessionInfo() R version 2.11.1 (2010-05-31) i386-apple-darwin9.8.0 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] goseq_1.0.3 geneLenDataBase_0.99.4 BiasedUrn_1.03 loaded via a namespace (and not attached): [1] AnnotationDbi_1.10.2 Biobase_2.8.0 biomaRt_2.4.0 Biostrings_2.16.9 BSgenome_1.16.5 DBI_0.2-5 [7] GenomicFeatures_1.0.6 GenomicRanges_1.0.6 grid_2.11.1 IRanges_1.6.8 lattice_0.18-8 Matrix_0.999375-39 [13] mgcv_1.6-2 nlme_3.1-96 RCurl_1.4-2 RSQLite_0.9-1 rtracklayer_1.8.1 tools_2.11.1 [19] XML_3.1-0 Has anyone else faced this problem in goseq? Any help is appreciated. Thanks, Joydeep
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