[BiO BB] gene expression software for mere biologists?

Harry Mangalam harry.mangalam at uci.edu
Tue Dec 23 17:22:49 EST 2008

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.


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: veredcc at bgu.ac.il
> Tel: 08-6479034 054-7915969
> Fax: 08-6472983
> http://bioinfo.bgu.ac.il
> ______________________________________________________________
> -----Original Message-----
> From: bbb-bounces at bioinformatics.org
> [mailto:bbb-bounces at bioinformatics.org] 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.]

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