[BioC] Cannot construct AnnotationDb for GOStats

[Marc Carlson]

Hi Hollis,

I want to help you but I cannot tell what went wrong from your partial 
posts (other than the fact that you are using a very old version of R).

   Marc



On 09/04/2012 12:44 PM, Hollis Wright wrote:
> 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)
>
> locale:
>   [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
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=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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