[BiO BB] gene expression software for mere biologists?

Vered Caspi veredcc at bgu.ac.il
Tue Dec 23 02:39:25 EST 2008

I highly recommend Partek, Spotfire (both commercial), Expander (mainly
clustering and functional analysis) and GSEA (functional analysis)

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

-----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
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 

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 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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