[BiO BB] gene expression software for mere biologists?

Yannick Wurm idh at poulet.org
Mon Dec 22 13:56:17 EST 2008

Hi Harry,

have you had a look at TIGR's MEV ?
it's limited compared to command-line tools, but definitely worth a  

also, some Bioconductor packages have GUIs: eg limmagui

But I think the bottom line is that "pure molecular" who want to do  
genome-scale experiments need to
	- either learn how to get around a commandline
	- or collaborate with someone who knows how to.


           yannick . wurm @ unil . ch
Ant Genomics, Ecology & Evolution @ Lausanne

On Dec 22, 2008, at 7:39 PM, Harry Mangalam wrote:

> 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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