Question

GOseq error on running nullp

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Entering edit mode

pereyra.s • 0

@pereyras-14106

Last seen 7.1 years ago

I am trying to run goseq package in R, working with human data with hg19. I followed the vignette instructions to create "gene.vector", but I am getting the following error:

> gene.vector <- as.integer(deseq.results$gene.id%in%genesDE)
> names(gene.vector) <- deseq.results$gene.id
> pwf=nullp(gene.vector,"hg19","ensGene")
Loading hg19 length data...
Error in smooth.construct.cr.smooth.spec(object, dk$data, dk$knots) :
  objeto 'C_crspl' no encontrado

Do you have a suggestion on how to solve the issue?

Thank you.

Current session info is as follows:

> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.2 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

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

other attached packages:
 [1] rtracklayer_1.36.4         goseq_1.28.0               geneLenDataBase_1.12.0     BiasedUrn_1.07             limma_3.32.7              
 [6] DESeq2_1.16.1              SummarizedExperiment_1.6.5 DelayedArray_0.2.7         matrixStats_0.52.2         Biobase_2.36.2            
[11] GenomicRanges_1.28.5       GenomeInfoDb_1.12.2        IRanges_2.10.3             S4Vectors_0.14.5           BiocGenerics_0.22.0

goseq GO term • 2.0k views

ADD COMMENT • link updated 7.1 years ago by Gordon Smyth 51k • written 7.1 years ago by pereyra.s • 0

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Please show us the complete output from sessionInfo(). The output that you give at the moment cannot be complete because you appear to have no packages loaded via a namespace. If I load goseq by itself into a clean R session, I see the following:

> library(goseq)
> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale:
[1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252   
[3] LC_MONETARY=English_Australia.1252 LC_NUMERIC=C                      
[5] LC_TIME=English_Australia.1252    

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

other attached packages:
[1] goseq_1.28.0           geneLenDataBase_1.12.0 BiasedUrn_1.07        

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.13               compiler_3.4.1             GenomeInfoDb_1.12.2       
 [4] XVector_0.16.0             GenomicFeatures_1.28.5     bitops_1.0-6              
 [7] tools_3.4.1                zlibbioc_1.22.0            biomaRt_2.32.1            
[10] digest_0.6.12              bit_1.1-12                 nlme_3.1-131              
[13] RSQLite_2.0                memoise_1.1.0              tibble_1.3.4              
[16] lattice_0.20-35            mgcv_1.8-22                pkgconfig_2.0.1           
[19] rlang_0.1.2                Matrix_1.2-11              DelayedArray_0.2.7        
[22] DBI_0.7                    parallel_3.4.1             GenomeInfoDbData_0.99.0   
[25] rtracklayer_1.36.4         Biostrings_2.44.2          S4Vectors_0.14.6          
[28] IRanges_2.10.4             stats4_3.4.1               bit64_0.9-7               
[31] grid_3.4.1                 Biobase_2.36.2             AnnotationDbi_1.38.2      
[34] XML_3.98-1.9               BiocParallel_1.10.1        GO.db_3.4.1               
[37] blob_1.1.0                 Rsamtools_1.28.0           matrixStats_0.52.2        
[40] GenomicAlignments_1.12.2   BiocGenerics_0.22.0        GenomicRanges_1.28.6      
[43] SummarizedExperiment_1.6.5 RCurl_1.95-4.8

Note especially that you have to see the mgcv package, because that is the package which contains the function that gave the error.

ADD REPLY • link 7.1 years ago Gordon Smyth 51k

score 2 · Accepted Answer · 2017-10-04

2

Entering edit mode

Gordon Smyth 51k

@gordon-smyth

Last seen 2 hours ago

WEHI, Melbourne, Australia

The code you give is a standard goseq function call and it normally runs correctly.

There appears to be a problem with your R session and how the packages (mgcv in particular) have been loaded. Try starting a fresh R session, load goseq again and try running the code again. The problem may disappear.

ADD COMMENT • link 7.1 years ago Gordon Smyth 51k

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Entering edit mode

That seemed to be the problem. mgcv package was missing. Starting a new session and loading goseq solved the issue.

Alternatively, loading the package mgcv in the same session also solved my problem.

Thank you very much for your help.

ADD REPLY • link 7.1 years ago pereyra.s • 0