[BioC] Problem with invalid GO term in HyperGResult object - NOT solved
rgentlem at fhcrc.org
Thu Sep 20 18:50:42 CEST 2007
We will have a look and see if something obvious has gone wrong...
any arabadopsis experts that might know something more should feel free
to venture an opinion here...
Jenny Drnevich wrote:
> Hi Herve,
> Thanks for letting me know the new Windows binaries were available.
> However, I traced the problem to the new annotation package for
> ath1121501 - it is USELESS for GOstats testing!! Arabidopsis doesn't use
> EntrezIDs, but instead uses AGI locus identifier, given in the
> ath1121501ACCNUM environment. This environment used to give unique IDs
> for almost all probe sets, but now all of the listings are either
> "multiple" or NA:
> > probes <- ls(ath1121501ACCNUM)
> > probes[1:10]
>  "244901_at" "244902_at" "244903_at" "244904_at" "244905_at"
>  "244906_at" "244907_at" "244908_at" "244909_at" "244910_s_at"
> > length(probes)
>  22810
> > locusList <- unique(unlist(mget(probes, ath1121501ACCNUM)))
> > length(locusList)
>  2
> > locusList
>  "multiple" NA
> I realize this is probably came from the Arabidopsis database used to
> create the annotation package, but is there any way to "fix" this, or to
> put up the older annotation package? The old one had a few hundred
> "multiple" entries, but I figured it wouldn't matter that much to throw
> them out. Any other ideas for ways around this problem?
> > sessionInfo()
> R version 2.6.0 Under development (unstable) (2007-08-28 r42679)
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
> attached base packages:
>  splines tools stats graphics grDevices utils datasets
>  methods base
> other attached packages:
>  limma_2.11.13 ath1121501_1.99.10 GOstats_2.3.17
>  Category_2.3.39 genefilter_1.15.11 survival_2.32
>  RBGL_1.13.6 annotate_1.15.11 xtable_1.5-1
>  GO.db_1.99.3 AnnotationDbi_0.99.1 RSQLite_0.6-2
>  DBI_0.2-3 graph_1.15.20 Biobase_1.15.34
> loaded via a namespace (and not attached):
>  cluster_1.11.7 simpleaffy_2.13.01
> 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
> ph: 217-244-7355
> fax: 217-265-5066
> e-mail: drnevich at uiuc.edu
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
rgentlem at fhcrc.org
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