[GeneX-dev] Re: [microarray-format] Mapping of Affy data to GeneX

[<ja...@op...>]

"Eric F. Tsung" <ef...@ch...> writes:

> I have been looking at the database that you help develop, GeneX,
> and will probably implement the Postgres part of it to store results
> we get from collaberators that my orginization analyzes.  I have set
> up GeneX on one of our servers.

Hey Eric,

I think that it's great that you're using GeneX. You may want to ask
for help or post information on the primary development list:

   gen...@li...

That way you'll get more attention.

Also I'm not sure what you mean by 'implement the Postgres part of
it'. The current GeneX schema is already a Postgres schema. Are you
talking about implementing a MAGE schema in Postgres? If so, that
would be great, but you would have to re-work all the tools, because
they are currently very schema-specific.

> Since GeneX first stored Affymetrix data, do you have a specific mapping
> of columns that come from Affy's .CHP and .CEL files into columns of the
> GeneX database.  I know that in general AM_Spots coorespond to the .CEL
> file and ArrayMeasurement, to the .CHP.

GeneX has been used to store Affy data, but only after analysis and
derivation. It wasn't until recently that I saw my first .CEL or .CHP
files, so I'm sorry but I don't have a mapping to give you.

I am currently seeking funding from a number of sources to build an
Open Source Affy data loader (as well as a spotted microarray
loader). We haven't heard back on the proposals yet, but we are
hopeful. In my mind the lack of an automateable loader is GeneX's
biggest weakness.

> Also, since I'm here in Boston, I'm very interested in attending
> MGED-4.  I'll keep checking the web site for updates.

Great! Let us know of your successes (or issues) with GeneX.

jas.