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Question: Error using goseq function in bioconductor pkg goseq
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gravatar for jdavison
2.7 years ago by
jdavison10
United States
jdavison10 wrote:

Using pkg goseq for the first time; I get this error:

> pwf = nullp(genes, 'hg19', 'Gene Symbol', bias.data=df$len)

Warning message:
In pcls(G) : initial point very close to some inequality constraints

> GO.wall = goseq(pwf, 'hg19', 'Gene Symbol')
Fetching GO annotations...
Error in if (coreid != userid) { : missing value where TRUE/FALSE needed

This may be a Oracle error?  I'm using version goseq 1.22.0.


> sessionInfo()

R version 3.1.3 (2015-03-09)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: Ubuntu 14.04.3 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods  
[9] base     

other attached packages:
 [1] org.Hs.eg.db_3.0.0    rtracklayer_1.26.3    GenomicRanges_1.18.4 
 [4] goseq_1.18.0          AnnotationDbi_1.28.2  GenomeInfoDb_1.2.4   
 [7] IRanges_2.0.1         S4Vectors_0.4.0       Biobase_2.26.0       
[10] BiocGenerics_0.12.1   RSQLite_1.0.0         DBI_0.3.1            
[13] geneLenDataBase_1.1.1 BiasedUrn_1.06.1      BiocInstaller_1.16.5 

loaded via a namespace (and not attached):
 [1] base64enc_0.1-2         BatchJobs_1.6           BBmisc_1.9             
 [4] BiocParallel_1.0.3      biomaRt_2.22.0          Biostrings_2.34.1      
 [7] bitops_1.0-6            brew_1.0-6              checkmate_1.5.3        
[10] codetools_0.2-11        compiler_3.1.3          digest_0.6.8           
[13] fail_1.2                foreach_1.4.2           GenomicAlignments_1.2.2
[16] GenomicFeatures_1.18.6  GO.db_3.0.0             grid_3.1.3             
[19] iterators_1.0.7         lattice_0.20-31         magrittr_1.5           
[22] Matrix_1.2-0            mgcv_1.8-6              nlme_3.1-120           
[25] RCurl_1.95-4.6          Rsamtools_1.18.3        sendmailR_1.2-1        
[28] stringi_0.4-1           stringr_1.0.0           tools_3.1.3            
[31] XML_3.98-1.1            XVector_0.6.0           zlibbioc_1.12.0  

ADD COMMENTlink modified 2.7 years ago by Gordon Smyth35k • written 2.7 years ago by jdavison10

Hi,

Try using "geneSymbol" rather than "Gene Symbol". Does your plot from nullp look reasonable? Can you post the result of "head(pwf)"? Also feel free to email me with data to reproduce this error if you like.

Cheers,

Nadia.

ADD REPLYlink written 2.6 years ago by Nadia Davidson270
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