Dear Harry, >Does Spotfire still support gene expression? It seems they do.
I am using SpotFire DecisionSite for Functional Genomics: http://spotfire.tibco.com/products/decisionsite_functional_genomics.cfm They also have a newer software with more advanced statistics for microarray analysis: SpotFire DecisionSite for Microarray Analysis: http://spotfire.tibco.com/solutions/life_sciences/biomarker_discovery.cfm With best regards, Vered ______________________________________________________________ Vered Caspi, Ph.D. Bioinformatics Core Facility, Head National Institute for Biotechnology in the Negev Building 39, room 214 Ben-Gurion University of the Negev Beer-Sheva 84105, Israel Email: [email protected] Tel: 08-6479034 054-7915969 Fax: 08-6472983 http://bioinfo.bgu.ac.il ______________________________________________________________ -----Original Message----- From: Harry Mangalam [mailto:[email protected]] Sent: Wednesday, December 24, 2008 12:23 AM To: [email protected] Cc: Vered Caspi Subject: Re: [BiO BB] gene expression software for mere biologists? Thanks very much for taking the time to comment. Does Spotfire still support gene expression? I went to their website but couldn't find anything related - it looks like they're trying to become SAS (business intelligence, decision support) just as SAS is trying to be Spotfire (with JMP/Genomics). Expander <http://acgt.cs.tau.ac.il/expander/> looks interesting - the 1st time I've heard of it. hjm On Monday 22 December 2008, Vered Caspi wrote: > Hello, > I highly recommend Partek, Spotfire (both commercial), Expander > (mainly clustering and functional analysis) and GSEA (functional > analysis) Vered > > ______________________________________________________________ > Vered Caspi, Ph.D. > Bioinformatics Core Facility, Head > National Institute for Biotechnology in the Negev > Building 39, room 214 > Ben-Gurion University of the Negev > Beer-Sheva 84105, Israel > > Email: [email protected] > Tel: 08-6479034 054-7915969 > Fax: 08-6472983 > > http://bioinfo.bgu.ac.il > ______________________________________________________________ > > -----Original Message----- > From: [email protected] > [mailto:[email protected]] On Behalf Of Harry Mangalam > Sent: Monday, December 22, 2008 8:40 PM > To: BBB > Subject: [BiO BB] gene expression software for mere biologists? > > Hi All, > > This may be a difficult query for this group to answer as the > readership is canted heavily in the geek direction, but what gene > expression software are you and your users relying on for gene > expression and pathway analysis? > > I tilt heavily towards R/Bioconductor and other free software, so > I'm aware of the advantages of it, but we have non-commandline tool > researchers who are in need of tools they can use to examine the > results of gene expression studies. > > This is something of a no-win - those tools that are very easy to > use tend to hide the very complexity that the user has to address, > and so the 'ease of use' / 'ease of thought' tends to weaken an > already iffy analysis. > > That said, are there tools (commercial or free) that provide fairly > good tradeoffs between power and ease of use for a non-geek > biologist user. ie runs on Mac & Windows and is mostly GUI? (If > you have experience in introducing such users to R, I'd also be > interested in your experiences). > > Due to some aggressive pushing from the local SAS consulting group, > we are in the startup phase of a campus-wide, 1 year trial of > JMP/Genomics. JMP is a fairly cheap, nicely designed, > multiplatform GUI stats package from SAS. The Genomics part tho is > an expensive add-on that runs only on Windows and depends on an > optional, even more expensive Pathways package from InGenuity. The > local research community does not have a problem paying for such > software if it truly does work easily and well. If you have used > it and have an opinion or evaluation, I'd love to hear from you via > email or phone. > > Harry -- Harry Mangalam - Research Computing, NACS, E2148, Engineering Gateway, UC Irvine 92697 949 824-0084(o), 949 285-4487(c) --- Good judgment comes from experience; Experience comes from bad judgment. [F. Brooks.] _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb
