Hi Jason,
There is a listserv dedicated to Bioconductor packages; I suggest you
post there.
[EMAIL PROTECTED]
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_1.16.1Biobase_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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