ReactomePA : error with gsePathway
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Entering edit mode
@samuel-collombet-6574
Last seen 4.4 years ago
France

Hi,

I would like to performed a continuous gsea with the ReactomePA, but I get the following result:

> y <- gsePathway(geneList_entrez, organism="mouse", nPerm = 100, minGSSize = 20,pvalueCutoff = 1, pAdjustMethod = "BH", exponent=1, verbose = T)
[1] "calculating observed enrichment scores..."
[1] "calculating permutation scores..."
  |============================================== |  99%
[1] "calculating p values..."
Error in .checkKeys(value, Lkeys(x), x@ifnotfound) : 
  value for "5604596" not found

my geneList seems well formated:

> head(geneList_entrez)
    18223     52428     67080     13056    225908    380684 
0.9999980 0.9999966 0.9999965 0.9999948 0.9999936 0.9999923 

I can reproduce the example in the vignette...
I thought it might be because my score are <1, but it doesn't work if I change them into the rank of the value.

> sessionInfo()
R version 3.1.0 RC (2014-04-05 r65382)
Platform: x86_64-pc-linux-gnu (64-bit)

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

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

other attached packages:
 [1] reactome.db_1.50.0        org.Mm.eg.db_3.0.0        topGO_2.18.0              SparseM_1.6               GO.db_3.0.0              
 [6] graph_1.44.1              biomaRt_2.22.0            Mfuzz_2.26.0              DynDoc_1.44.0             widgetTools_1.44.0       
[11] e1071_1.6-4               wq_0.4-1                  zoo_1.7-12                reshape2_1.4.1            ggplot2_1.0.1            
[16] RColorBrewer_1.1-2        DESeq2_1.6.3              RcppArmadillo_0.4.650.1.1 Rcpp_0.11.5               GenomicRanges_1.18.4     
[21] org.Hs.eg.db_3.0.0        ReactomePA_1.10.1         DOSE_2.4.0                AnnotationDbi_1.28.2      GenomeInfoDb_1.2.4       
[26] IRanges_2.0.1             S4Vectors_0.4.0           Biobase_2.26.0            BiocGenerics_0.12.1       RSQLite_1.0.0            
[31] DBI_0.3.1                

loaded via a namespace (and not attached):
 [1] acepack_1.3-3.3     annotate_1.44.0     base64enc_0.1-2     BatchJobs_1.6       BBmisc_1.9          BiocParallel_1.0.3  bitops_1.0-6       
 [8] brew_1.0-6          checkmate_1.5.2     class_7.3-12        cluster_2.0.1       codetools_0.2-11    colorspace_1.2-6    digest_0.6.8       
[15] DO.db_2.8.0         fail_1.2            foreach_1.4.2       foreign_0.8-63      Formula_1.2-0       genefilter_1.48.1   geneplotter_1.44.0 
[22] GOSemSim_1.24.1     graphite_1.12.0     gtable_0.1.2        Hmisc_3.15-0        igraph_0.7.1        iterators_1.0.7     lattice_0.20-30    
[29] latticeExtra_0.6-26 locfit_1.5-9.1      MASS_7.3-40         munsell_0.4.2       nnet_7.3-9          plyr_1.8.1          proto_0.3-10       
[36] qvalue_1.43.0       RCurl_1.95-4.5      rpart_4.1-9         scales_0.2.4        sendmailR_1.2-1     splines_3.1.0       stringr_0.6.2      
[43] survival_2.38-1     tkWidgets_1.44.0    tools_3.1.0         XML_3.98-1.1        xtable_1.7-4        XVector_0.6.0     
ReactomePA gsePathway • 1.5k views
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Guangchuang Yu ★ 1.2k
@guangchuang-yu-5419
Last seen 8 months ago
China/Guangzhou/Southern Medical Univer…

Hi Samuel,

This is an known issue, please refer to reactome.db is not updated? .

This issue is not caused by ReactomePA, but due to reactome.db. I don't know why reactome are not responsive this time. The current release of reactome.db is not correct and hopefully they will offer right data in next release.

Currently, you can manual install the old version of reactome.db, http://www.bioconductor.org/packages/2.14/data/annotation/html/reactome.db.html, and everything will be OK.

 

Bests,

Guangchuang

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Now it works fine :) Thanks!

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Entering edit mode
Guangchuang Yu ★ 1.2k
@guangchuang-yu-5419
Last seen 8 months ago
China/Guangzhou/Southern Medical Univer…

BTW: you may interesting in GSEA analysis with latest online KEGG data using clusterProfiler, http://ygc.name/2015/02/01/kegg-enrichment-analysis-with-latest-online-data-using-clusterprofiler/ .

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Great Thanks! I haven't tried clusterProfiler yet, will do :)

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