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Re: Significant Gene expression analysis in Mathematica

• To: mathgroup at smc.vnet.net
• Subject: [mg122619] Re: Significant Gene expression analysis in Mathematica
• From: Zach Bjornson <zachb at wolfram.com>
• Date: Thu, 3 Nov 2011 03:47:52 -0500 (EST)
• Delivered-to: l-mathgroup@mail-archive0.wolfram.com
• References: <j8r97d$3h7$1@smc.vnet.net>

On 11/2/2011 4:23 AM, Jay romero wrote:
> Hi
>
> I have been trying to find out how one can do " Significant Gene
> expression analysis in Mathematica".
> Is it possible in Mathematica? or I have to use R?
>
> Jay Romero
>

Greetings,

Most of the analysis tools commonly used for gene expression analysis 
exist in Mathematica. I'd take a look at the resources in 
<<HierarchicalClustering and the hypothesis testing tools. The National 
Cancer Institute has written a comprehensive package in Mathematica 7 
for microarray analysis:
http://prevention.cancer.gov/programs-resources/groups/b/software/swirls

I find it useful to be able to access gene ontology from GenomeData or 
W|A live queries, if your data isn't annotated with GO terms yet.

Mathematica has an Affymetrix microarray importer. You can also import 
Agilent microarray data as a TSV.

Finally, if you want to access R functions (e.g. bioconductor tools) 
from Mathematica, here is a MathGroup post about doing so:
http://forums.wolfram.com/mathgroup/archive/2009/Jun/msg00415.html

The NETLink docs can be found here in the Documentation Center:
NETLink/tutorial/Overview

And this is the website for ScienceOps application:
http://www.scienceops.com/Rlink2.asp

Hope that helps. I'm happy to answer more specific questions.

Best,
Zach
Wolfram|Alpha Biology