[BioC] Error in package goseq
joy.mitra at yahoo.com
Tue Aug 17 20:52:04 CEST 2010
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:
Using manually entered categories.
Error in summary(map)[, 1] : incorrect number of dimensions
Here's my session info:
R version 2.11.1 (2010-05-31)
attached base packages:
 stats graphics grDevices utils datasets methods base
other attached packages:
 goseq_1.0.3 geneLenDataBase_0.99.4 BiasedUrn_1.03
loaded via a namespace (and not attached):
 AnnotationDbi_1.10.2 Biobase_2.8.0 biomaRt_2.4.0
Biostrings_2.16.9 BSgenome_1.16.5 DBI_0.2-5
 GenomicFeatures_1.0.6 GenomicRanges_1.0.6 grid_2.11.1
IRanges_1.6.8 lattice_0.18-8 Matrix_0.999375-39
 mgcv_1.6-2 nlme_3.1-96 RCurl_1.4-2
RSQLite_0.9-1 rtracklayer_1.8.1 tools_2.11.1
Has anyone else faced this problem in goseq? Any help is appreciated.
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