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@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I searched geneontology.org, and this GO term is outdated(?)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@uiuc.edu 
	[[alternative HTML version deleted]]

