[Bioperl-l] microarray analysis in perl

[Kass Schmitt]

In message <Pine.OSF.4.10.10103080447080.6546-100000@is06.fas.harvard.edu>, Fin
ny Kuruvilla wrote:
>We've been thinking about writing a more elegant solution to tackle
>these kinds of issues and I was thinking about using MySQL/Perl to do
>so.  I saw on your list of projects that although microarray analysis
>was listed, that no one was working on it at the moment.  In fact, the
>site reads, "This is a rapidly moving field and it may be a while
>before standards emerge. Perl may not be best for analysis of array
>data."
>
>Coming from more of a Matlab/Lisp background myself (no Perl expert),
>I'm hoping for some insights from some of you.  First, do you think
>that Perl is the right language for this?  If not, what do think would
>work best?  What open-source efforts do you know that are going on
>right now in this?

We are currently working on a microarray project called TANGO
(Transcriptome ANalsysis of GenOmes) in collaboration with Alexander
Sczyrba and Mathias Katzer at Bielefeld University.  Although it is
not currently open source it appears to be headed in that direction.

For the heavy-duty analysis we are using R.
(following the Speed Group's lead:
http://www.stat.berkeley.edu/users/terry/zarray/Html/soft.html)
 
We are using PostgreSQL for our db, and perl to glue it all together.

I'll post more details when I know for sure what's happening with the
project.

best,
Kass

--
Kathryn Schmitt, Research Programmer		
The Gaasterland Lab for Computational Genomics
The Rockefeller University
schmitt@mistral.rockefeller.edu		
(212) 327-7785