Question: Where are the broadsets for GSEA?
0
gravatar for peter robinson
11.6 years ago by
peter robinson300 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") fails > if (!exists("broadsets")) load("broadsets.rda") Fehler in readChar(con, 5) : kann Verbindung nicht ?ffnen Zus?tzlich: Warning message: In readChar(con, 5) : cannot open compressed file 'broadsets.rda', probable reason 'Datei oder Verzeichnis nicht gefunden' > My session info; > sessionInfo() R version 2.6.2 (2008-02-08) i486-pc-linux-gnu locale: LC_CTYPE=de_DE at euro;LC_NUMERIC=C;LC_TIME=de_DE at euro;LC_COLLATE=de_DE at euro;LC_MONETARY=de_DE at euro;LC_MESSAGES=de_DE at euro;LC_PAPER=de_DE at euro;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=de_DE at euro;LC_IDENTIFICATION=C attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] GSEABase_1.0.3 AnnotationDbi_1.0.6 RSQLite_0.6-4 [4] DBI_0.2-4 Biobase_1.16.1 loaded via a namespace (and not attached): [1] rcompgen_0.1-17 XML_1.93-2 > Thanks for any advice, Peter
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ADD COMMENTlink modified 11.6 years ago by Martin Morgan ♦♦ 24k • written 11.6 years ago by peter robinson300
Answer: Where are the broadsets for GSEA?
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gravatar for Martin Morgan
11.6 years ago by
Martin Morgan ♦♦ 24k
United States
Martin Morgan ♦♦ 24k wrote:
"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 e.g., > 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). Martin > Sean > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Martin Morgan 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
ADD COMMENTlink written 11.6 years ago by Martin Morgan ♦♦ 24k
Answer: Where are the broadsets for GSEA?
0
gravatar for Sean Davis
11.6 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
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. Sean
ADD COMMENTlink written 11.6 years ago by Sean Davis21k
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