Re: [R] Help with 'annotation' in GOHyperGParamsClass

From: James W. MacDonald <jmacdon_at_med.umich.edu>
Date: Mon, 03 Nov 2008 10:01:16 -0500

Hi Jason,

There is a listserv dedicated to Bioconductor packages; I suggest you post there.

bioconductor_at_stat.math.ethz.ch

Best,

Jim

Jason Myers wrote:
> Dear cateGOry experts,
> hyperGTest documentation states that YEAST cannot be used as 'annotation'
> when evaluating gene ontology representation status for a given set of
> 'geneIds'.
>
> Because I am using a custom print I believe I need to create my own data
> package to use as the annotation file for 'annotation'. Can someone please
> describe how to make a data package that will be compatible with the
> 'annotation' required for proper function of hyperGTest?
>
> Session Info below,
>
> Thanks,
>
> Jason
>
>

>> sessionInfo()

> R version 2.6.2 (2008-02-08)
> i386-apple-darwin8.10.1
>
> locale:
> en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] splines tools stats graphics grDevices utils datasets
> methods base
>
> other attached packages:
> [1] GOstats_2.4.0 RBGL_1.14.0 geneplotter_1.16.0
> lattice_0.17-4 limma_2.12.0
> [6] org.Sc.sgd.db_2.0.2 YEAST_2.0.1 GO.db_2.0.2 DAAG_0.95
> MASS_7.2-40
> [11] Category_2.4.0 genefilter_1.16.0 survival_2.34
> annotate_1.16.1 xtable_1.5-2
> [16] AnnotationDbi_1.0.6 RSQLite_0.6-4 DBI_0.2-4
> graph_1.16.1 Biobase_1.16.3
> [21] GO_2.0.1
>
> loaded via a namespace (and not attached):
> [1] KernSmooth_2.22-22 RColorBrewer_1.0-2 cluster_1.11.9 grid_2.6.2
>
-- 
James W. MacDonald, M.S.
Biostatistician
Hildebrandt Lab
8220D MSRB III
1150 W. Medical Center Drive
Ann Arbor MI 48109-0646
734-936-8662

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Received on Mon 03 Nov 2008 - 15:04:19 GMT

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