[R] Help with 'annotation' in GOHyperGParamsClass

From: Jason Myers <dr.jason.myers_at_gmail.com>
Date: Sun, 02 Nov 2008 21:12:11 -0800

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,



> sessionInfo()
R version 2.6.2 (2008-02-08)


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

[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

Jason Myers

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Received on Mon 03 Nov 2008 - 05:17:26 GMT

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