[BioC] hyperGTest on proteomics data

[Kimpel, Mark William]

Seth,

Thanks for your offer of help on this. I am very much a novice compared
to you, but I would be happy to help with coding to move things along at
some point. This is not an urgent issue for me, as we are going to
submit a grant in a week, so will just outline our methods for now.

Mark

Mark W. Kimpel MD 

 

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-----Original Message-----
From: Seth Falcon [mailto:sfalcon at fhcrc.org] 
Sent: Monday, January 22, 2007 12:06 PM
To: Kimpel, Mark William
Cc: bioconductor at stat.math.ethz.ch; Seth Falcon
Subject: Re: hyperGTest on proteomics data

"Kimpel, Mark William" <mkimpel at iupui.edu> writes:
> I would like to use the hyperGTest in package "GOstats" on some
> proteomics data that I have. It is LCMS data and I have a list of all
> Entrez Gene identifiers of all identified proteins (the universe) and
of
> the significant proteins. 

> I imagine this is because hyperGTest relies on the Bioc metadata
> packages to map EntrezGene to GO categories. It seems to me that there
> should be a work around to this problem using biomaRt or some direct
> calls to the GO website.

Your assessment is correct.  The code in Category and GOstats relies
upon environments from an annotation data package to retrieve the
required mappings.

It should be possible to obtain the mappings required for the test
using just the GO package, but it will require some work...

> Suggestions?

I think the way to go is to add either a new parameter class and/or a
new class for representing the annotation data (in devel there is
already code along these lines to make use of SQLite-based annotation
packages).

Then one would need to define methods for universeBuilder and
categoryToEntrezBuilder that extract the required info just using the
GO package.

At that point, things should plug into the rest of the code and Just
Work (yeah, sure).

It is something that is on my TODO list, but I don't have an ETA for
when it will be done.

+ seth