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Question: ReactomePA : error with gsePathway
0
gravatar for samuel collombet
2.7 years ago by
France
samuel collombet100 wrote:

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     
ADD COMMENTlink modified 2.7 years ago by Guangchuang Yu800 • written 2.7 years ago by samuel collombet100
1
gravatar for Guangchuang Yu
2.7 years ago by
Hong Kong
Guangchuang Yu800 wrote:

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

ADD COMMENTlink written 2.7 years ago by Guangchuang Yu800

Now it works fine :) Thanks!

ADD REPLYlink modified 2.7 years ago • written 2.7 years ago by samuel collombet100
1
gravatar for Guangchuang Yu
2.7 years ago by
Hong Kong
Guangchuang Yu800 wrote:

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/ .

ADD COMMENTlink written 2.7 years ago by Guangchuang Yu800

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

ADD REPLYlink written 2.7 years ago by samuel collombet100
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