[Bioperl-l] microarray analysis in perl

[Finny Kuruvilla]

I'm a biologist/programmer who has been doing microarray work the past
couple years. (For the type of work, look on Pubmed for Current
Biology 2000; 10(24): 1574-1581, Proc Natl Acad Sci USA. 1999;
96(26):14866-70 if anyone is interested.)  In the course of analyzing
data we've generated, I've written code in languages like Visual Basic
and Matlab.  But my efforts have been non-systematic thus far.

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?

To me the time seems ripe to tackle these issues, but I would really
appreciate any advice (truly -- anything at all) that those of you
more experienced could offer.

Thanks.

Finny 

*****************************************************************
Finny Kuruvilla
MD-PhD Program, Harvard Medical School
Schreiber Group, Department of Chemistry and Chemical Biology
Harvard University -- Cambridge, Massachusetts
kuruvill@fas.harvard.edu