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