[BioC] Where are the broadsets for GSEA?

Martin Morgan 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
>> here:
>>  http://www.biostat.harvard.edu/%7Ecarey/bos08bct/pathcase.pdf
>>  however,
>>  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


> 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).


> Sean
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Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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