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
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
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
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
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