[BioC] Cannot construct AnnotationDb for GOStats

Hollis Wright wrighth at ohsu.edu
Tue Sep 4 21:44:33 CEST 2012

Sorry for double post, hit send accidentally. Basically, any workaround for this other than to pull specific evidence codes? I am stuck on R 2.13 for the moment; tried updating AnnotationDbi via biocLite but no luck. Thanks...

Hollis Wright, PhD
Ojeda Lab, Division of Neuroscience
Oregon Health and Science University
From: Hollis Wright
Sent: Tuesday, September 04, 2012 12:44 PM
To: bioconductor at r-project.org
Subject: Cannot construct AnnotationDb for GOStats

Hi, all; I'm running into some gremlins trying to get together a custom db object to run GOstats on some Affy exon 1.0 data. Specifically, I'm following the instructions in the GOStatsForUnsupportedOrganisms.pdf. We've rolled up expression to Ensembl identifiers, so I've used biomaRt to pull the evidence codes and identifiers thus:

go_id Evidence         gene_id
1  GO:0016567      IEA ENSG00000259662
2  GO:0005515      IEA ENSG00000259662
3  GO:0055114      IEA ENSG00000258865
4  GO:0004800      IEA ENSG00000258865
5  GO:0005576      IEA ENSG00000261933
10 GO:0007049      IEA ENSG00000227268

but when I

R version 2.13.0 (2011-04-13)
Platform: x86_64-unknown-linux-gnu (64-bit)

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] GO.db_2.5.0          GOstats_2.18.0       RSQLite_0.9-4
[4] DBI_0.2-5            graph_1.30.0         Category_2.18.0
[7] AnnotationDbi_1.14.1 Biobase_2.12.1

loaded via a namespace (and not attached):
 [1] annotate_1.30.0   bestglm_0.33      genefilter_1.34.0 GSEABase_1.14.0
 [5] leaps_2.9         RBGL_1.28.0       splines_2.13.0    survival_2.36-5
 [9] tools_2.13.0      XML_3.4-0         xtable_1.5-6

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