[Biojava-l] Gene Expression

[Matthew Pocock]

Jason Stajich wrote:

> I'm sure Matt will respond to this effect but check out
> http://www.sanger.ac.uk/Users/mrp/java/ExpressionBrowser/
>
> Bioinformatics, Vol 16, no. 4 2000
> Pages 402 - 403
> [ if you have online access to the bioinformatics journal these should
> work ]
>
> http://bioinformatics.oupjournals.org/cgi/content/abstract/16/4/402
> http://bioinformatics.oupjournals.org/cgi/reprint/16/4/402
>
> -Jason
>

Thanks for the plug Jason :-)


>
> On Mon, 24 Jul 2000, Alex Tolley wrote:
>
> > Hi,
> >    I am in the process of building some beans to analyse gene array
> > expression data.  If you are going down that track as you imply, do you
> > have any data structures for this in the pipline?  I would like my code
> > to be inter-operable with yours where possible as I am getting very fed
> > up reinventing the wheel.

The data-structures that I came up with were messy, hacky things that I
ported from Perl. The visual display was nice though. The code for my
expression browser is LGPLed, so feel free to pillage anything that looks
usefull. Some of it should meander into BioJava as-and-when.

What data structures have you come up with so far? I know that there are
others on the list with code and/or ideas for this already, so it would be
realy good to get something hammered out.

An expression level is measured for a particular probe (spot on micro-array,
primer pair in quantative PCR), and a particular condition (glucose level,
temprature, delta-time...). A full experiment is a (possibly sparse) matrix
of probe vs conditions. The expression level itself has a level and possibly
lots of other stuff - optical intencity, evenness, error-margins. Many forms
of measurement have images associated with sub-sets of the data - gell images
for 1 primer pair over 12 conditions, or one didgitised micro-array.

Basicaly, some of these units will be usefull to everybody, so if anybody has
a plan for what any of these look like, then please propose it.

Matthew

>
> >
> > Regards,
> >
> > --
> > ==============================================
> > Alex Tolley
> > Snr. Software Engineer, Computational Sciences
> > Iconix Pharmaceuticals
> > 850 Maude Ave, Mountain View, CA 94043
> >
> > e-mail: atolley@iconixpharm.com
> >
> >
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l@biojava.org
> > http://biojava.org/mailman/listinfo/biojava-l
> >
>
> Jason Stajich
> jason@chg.mc.duke.edu
> http://galton.mc.duke.edu/~jason/
> (919)684-1806 (office)
> (919)684-2275 (fax)
> Center for Human Genetics - Duke University Medical Center
> http://wwwchg.mc.duke.edu/
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l

--
Joon: You're out of your tree
Sam:  It wasn't my tree
                                                 (Benny & Joon)