ReactomPA error using viewPathway
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@emiliomastriani-11983
Last seen 4.1 years ago

Hello

I tried to use the ReactomePA package and everything looks good, but finally I got the following error:

 

> viewPathway("E2F mediated regulation of DNA replication", readable=TRUE, foldChange=CL5_geneList)
'select()' returned 1:1 mapping between keys and columns
'select()' returned 1:1 mapping between keys and columns
Error: !any(duplicated(names(foldChange))) is not TRUE

My session:

> sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.4 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             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] graphite_1.20.1           reactome.db_1.58.0        ReactomePA_1.18.1        
 [4] DOSE_3.0.9                GO.db_3.4.0               ggrepel_0.6.5            
 [7] beadarray_2.24.0          ggplot2_2.2.0             illuminaHumanv3.db_1.26.0
[10] org.Hs.eg.db_3.4.0        limma_3.30.7              GEOquery_2.40.0          
[13] GeneAnswers_2.16.0        RColorBrewer_1.1-2        Heatplus_2.20.0          
[16] MASS_7.3-45               RSQLite_1.1-1             annotate_1.52.1          
[19] XML_3.98-1.5              AnnotationDbi_1.36.0      IRanges_2.8.1            
[22] S4Vectors_0.12.1          Biobase_2.34.0            BiocGenerics_0.20.0      
[25] RCurl_1.95-4.8            bitops_1.0-6              igraph_1.0.1             

loaded via a namespace (and not attached):
 [1] qvalue_2.6.0         fgsea_1.0.2          reshape2_1.4.2       splines_3.3.2       
 [5] colorspace_1.3-2     BeadDataPackR_1.26.0 RBGL_1.50.0          DBI_0.5-1           
 [9] rappdirs_0.3.1       BiocParallel_1.8.1   plyr_1.8.4           stringr_1.1.0       
[13] zlibbioc_1.20.0      munsell_0.4.3        GOSemSim_2.0.3       gtable_0.2.0        
[17] memoise_1.0.0        labeling_0.3         GenomeInfoDb_1.10.1  illuminaio_0.16.0   
[21] Rcpp_0.12.8          xtable_1.8-2         openssl_0.9.5        scales_0.4.1        
[25] DO.db_2.9            base64_2.0           graph_1.52.0         XVector_0.14.0      
[29] gridExtra_2.2.1      fastmatch_1.0-4      digest_0.6.10        stringi_1.1.2       
[33] GenomicRanges_1.26.1 grid_3.3.2           tools_3.3.2          magrittr_1.5        
[37] lazyeval_0.2.0       tibble_1.2           data.table_1.10.0    downloader_0.4      
[41] assertthat_0.1       httr_1.2.1           R6_2.2.0 

 

I hope that someone can help me.

Best thanks,

Emilio

 

 

ReactomePA reactome Bioconductor viewPathway • 578 views
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Entering edit mode
Guangchuang Yu ★ 1.2k
@guangchuang-yu-5419
Last seen 9 months ago
China/Guangzhou/Southern Medical Univer…
Error: !any(duplicated(names(foldChange))) is not TRUE

 

your geneList, CL5_geneList, contains duplicated name.

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