Bingo, thank you and romer ran These missing little tidbits can be brutal > From: Martin Morgan <mtmorgan at="" fhcrc.org=""> > Date: Wed, 05 May 2010 05:11:02 -0700 > To: Loren Engrav <engrav at="" u.washington.edu=""> > Cc: rbioc <bioconductor at="" stat.math.ethz.ch=""> > Subject: Re: [BioC] Romer and symbols2indices query > > On 05/04/2010 07:57 PM, Loren Engrav wrote: >> Am back >> >> So I have romer and GSEABase running via previous help thank you, but while >> running I explore GSEABase >> >> And I have a lesser question for interest >> >> In GSEABase I do >> gmtObject <- getGMT("c2all.v2.5.symbols.gmt", >> collectionType=BroadCollection(category="c2"), geneType=SymbolIdentifier()) > > or maybe getBroadSets ? > >> which finishes without error >> Then >> class(gmtObject) is GeneSetCollection >> >> How do I convert gmtObject to a list of gene sets as required in romer when >> using > > gmtl <- geneIds(gmtObject) > names(gmtl) <- names(gmtObject) > > ? > > Martin > >> X <- symbols2indices (ListOfGeneSets, MYsymbols) >> >> >> >> From: Vincent Carey <stvjc at="" channing.harvard.edu=""> >> Date: Tue, 4 May 2010 11:40:39 -0400 >> To: Loren Engrav <engrav at="" u.washington.edu=""> >> Cc: rbioc <bioconductor at="" stat.math.ethz.ch=""> >> Subject: Re: [BioC] Romer and symbols2indices query >> >> Very briefly, the GSEABase package has relevant utilities for gmt file >> import/export and may be worth considering for these tasks. >> >> On Tue, May 4, 2010 at 10:43 AM, Loren Engrav <engrav at="" u.washington.edu=""> >> wrote: >>> Thank you, got it >>> >>> Downloading rdata objects saves reading them into an rdata object, cool >>> >>> But for interest, in R/GSA there is >>> GSA.read.gmt(filename.gmt) to read in a .gmt file >>> >>> Does limma or romer have an equivalent function? >>> >>> >>>> From: Matthew Ritchie <mritchie at="" wehi.edu.au=""> >>>> Date: Tue, 4 May 2010 14:44:23 +1000 (EST) >>>> To: Loren Engrav <engrav at="" u.washington.edu=""> >>>> Cc: rbioc <bioconductor at="" stat.math.ethz.ch=""> >>>> Subject: Re: [BioC] Romer and symbols2indices query >>>> >>>> Dear Loren, >>>> >>>> You can find rdata objects of the Broad's MSigDB gene sets at >>>> >>>> http://bioinf.wehi.edu.au/software/MSigDB/index.html >>>> >>>> You are right, the 'symbols' argument in the function symbols2indicies() >>>> are the gene symbols corresponding to the probes from your microarray >>>> data. >>>> >>>> For example, to use the human C2 collection, download the rdata file, then >>>> run the following. >>>> >>>> load("human_c2.rdata") >>>> c2 = symbols2indices(Hs.gmtl.c2, symbols) >>>> >>>> (this assumes 'symbols' is a vector containing the gene symbols from your >>>> array data) >>>> >>>> Best wishes, >>>> >>>> Matt >>>> >>>>> Have done GSEA and GSA for set enrichment and am setting out to try romer >>>>> and have probably "simple" question >>>>> >>>>> To get the Broad set into a list of indices there is >>>>> symbols2indices(gmtl.official, symbols) but >>>>> >>>>> 1)how do I get the Broad set into gmtl.official? And >>>>> 2)is symbols a vector of MY probe sets of interest? >>>>> >>>>> I checked gmane and found only one comment about romer >>>>> Also checked limma reference pdf >>>>> >>>>> Thank you >>>> >>>> >>>> ______________________________________________________________________ >>>> The information in this email is confidential and inte...{{dropped:7}} >>> >>> _______________________________________________ >>> 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 >> >> _______________________________________________ >> 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 M1 B861 > Phone: (206) 667-2793