Question: GOseq error on running nullp
0
gravatar for pereyra.s
2.0 years ago by
pereyra.s0
pereyra.s0 wrote:

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 • 497 views
ADD COMMENTlink modified 2.0 years ago by Gordon Smyth38k • written 2.0 years ago by pereyra.s0

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 REPLYlink modified 2.0 years ago • written 2.0 years ago by Gordon Smyth38k
Answer: GOseq error on running nullp
2
gravatar for Gordon Smyth
2.0 years ago by
Gordon Smyth38k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth38k wrote:

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 COMMENTlink modified 2.0 years ago • written 2.0 years ago by Gordon Smyth38k

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 REPLYlink written 2.0 years ago by pereyra.s0
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