[BioC] Where are the broadsets for GSEA?
mtmorgan at fhcrc.org
Sun May 4 17:19:52 CEST 2008
"Sean Davis" <sdavis2 at mail.nih.gov> writes:
> On Sat, May 3, 2008 at 9:53 AM, Peter Robinson
> <peter.robinson at t-online.de> wrote:
>> Hi all,
>> I would like to try the tutorial on gene set enrichment analysis as given
>> if (!exists("broadsets")) load("broadsets.rda")
> Hi, Peter. You will need to download the .xml file from the Broad
> after logging into their site. You can then refer to the Vignette for
> GSEABase for an example of how to make a Broad Set Collection given
> the location of the xml file on your disk.
Actually, sets from the Broad should be accessible using the example
on the 'getBroadSets' help page
> getBroadSets(asBroadUri(c('chr16q', 'GNF2_ZAP70')))
I'm not sure where the specific Broad set in the referenced pdf can be
found. This is with GSEABase 1.0.3 in R 2.6.2 (or later).
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M2 B169
Phone: (206) 667-2793
More information about the Bioconductor