[BioC] Problem with invalid GO term in HyperGResult object

[Jenny Drnevich]

Hi again,

I posted this message last week, but didn't get any responses. I've 
been trying everything I can think of to remove this one problematic 
GO term from my HyperGResult object so I can get the other 45 
overrepresented GO terms, but I'm not having any luck. I would 
appreciate any suggestions!!!

Thank  you,
Jenny


At 12:22 PM 9/5/2007, Jenny Drnevich wrote:
>Hi everyone,
>
>I'm doing hypergeometric testing of GO terms using GOstats on some
>data from ath1121501 Affy arrays. I had some trouble figuring out how
>to work with these arrays at first because the annotation package
>doesn't include EntrezIDs, but after searching the archives I found
>all you had to do was this to get it to work:
>
>ath1121501ENTREZID <- ath1121501ACCNUM
>
>Anyway, everything was going fine, expect in one my HyperGResult
>objects there is a significant GO term that throws up an error:
>
>  >SVC.up.BP <- new("GOHyperGParams", geneIds =
>entrezUniverse.sortVctrl[EID.sortVctrl==1],
>                  universeGeneIds = entrezUniverse.sortVctrl,
>annotation = "ath1121501",
>                  ontology = "BP", pvalueCutoff = hgCutoff, 
> conditional = FALSE,
>                  testDirection = "over")
>
>  >SVC.up.BP.results <- hyperGTest(SVC.up.BP)
>
>  >summary(SVC.up.BP.results)
>Error in .checkKeys(value, Lkeys(x), x at ifnotfound) :
>    invalid key "GO:0002226"
>
>I searched geneontology.org, and this GO term is outdated(?) because
>it's a synonym for
><http://amigo.geneontology.org/cgi-bin/amigo/go.cgi?view=details&search_constraint=terms&depth=0&query=GO:0045087&session_id=5451b1189011569>innate 
>
>immune response ; GO:0045087.  My question is: what's the easiest way
>to get around this error so I can get the rest of the output using
>summary() and htmlReport()? I tried subsetting the HyperGResults
>object to remove this one term, but it's not subsettable. Is there a
>way to replace the invalid GO term with the hopefully good synonym term?
>
>Thanks,
>Jenny
>
>  > sessionInfo()
>R version 2.6.0 Under development (unstable) (2007-08-28 r42679)
>i386-pc-mingw32
>
>locale:
>LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
>States.1252;LC_MONETARY=English_United
>States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>
>attached base packages:
>[1] splines   tools     stats     graphics  grDevices utils     datasets
>[8] methods   base
>
>other attached packages:
>   [1] ath1121501_1.17.0      Rgraphviz_1.15.5       hgu95av2.db_1.17.3
>   [4] ALL_1.4.3              affyQCReport_1.15.3    geneplotter_1.15.9
>   [7] lattice_0.16-3         RColorBrewer_1.0-1     simpleaffy_2.13.01
>[10] made4_1.11.1           scatterplot3d_0.3-24   ade4_1.4-3
>[13] affyPLM_1.13.6         affydata_1.11.3        affycoretools_1.9.4
>[16] annaffy_1.9.1          KEGG_1.17.0            GO_1.17.0
>[19] xtable_1.5-1           gcrma_2.9.1            matchprobes_1.9.10
>[22] biomaRt_1.11.4         RCurl_0.8-1            XML_1.9-0
>[25] GOstats_2.3.16         Category_2.3.30        genefilter_1.15.11
>[28] survival_2.32          RBGL_1.13.6            annotate_1.15.6
>[31] GO.db_1.17.1           AnnotationDbi_0.1.12   RSQLite_0.6-2
>[34] DBI_0.2-3              graph_1.15.14          limma_2.11.11
>[37] affy_1.15.7            preprocessCore_0.99.12 affyio_1.5.8
>[40] Biobase_1.15.30
>
>loaded via a namespace (and not attached):
>[1] cluster_1.11.7     grid_2.6.0         KernSmooth_2.22-21
>
>
>
>Jenny Drnevich, Ph.D.
>
>Functional Genomics Bioinformatics Specialist
>W.M. Keck Center for Comparative and Functional Genomics
>Roy J. Carver Biotechnology Center
>University of Illinois, Urbana-Champaign
>
>330 ERML
>1201 W. Gregory Dr.
>Urbana, IL 61801
>USA
>
>ph: 217-244-7355
>fax: 217-265-5066
>e-mail: drnevich at uiuc.edu
>         [[alternative HTML version deleted]]
>
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