[BioC] Problem with invalid GO term in HyperGResult object - NOT solved

[Jenny Drnevich]

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]
  [1] "244901_at"   "244902_at"   "244903_at"   "244904_at"   "244905_at"
  [6] "244906_at"   "244907_at"   "244908_at"   "244909_at"   "244910_s_at"
 > length(probes)
[1] 22810
 > locusList <- unique(unlist(mget(probes, ath1121501ACCNUM)))
 > length(locusList)
[1] 2
 > locusList
[1] "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?

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] limma_2.11.13        ath1121501_1.99.10   GOstats_2.3.17
  [4] Category_2.3.39      genefilter_1.15.11   survival_2.32
  [7] RBGL_1.13.6          annotate_1.15.11     xtable_1.5-1
[10] GO.db_1.99.3         AnnotationDbi_0.99.1 RSQLite_0.6-2
[13] DBI_0.2-3            graph_1.15.20        Biobase_1.15.34

loaded via a namespace (and not attached):
[1] 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
USA

ph: 217-244-7355
fax: 217-265-5066
e-mail: drnevich at uiuc.edu