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[Arabidopsis] question for microarray/co-expression developers - frma for ATH1?

Loraine, Ann via arab-gen%40net.bio.net (by Ann.Loraine from uncc.edu)
Fri Oct 4 14:38:03 EST 2013


Hello all,

My lab develops cressexpress.org, a microarray data-mining service for
Arabidopsis.

We're in the process of updating the site and have run into the not-very
surprising problem of running out of memory when attempting to use RMA to
process 8000+ ATH1 arrays from GEO.

The frma approach seems like a better way to do this but it looks like
there is no 
publicly available data file for the ATH1/GPL198 array.

To give some background, the frma ("frozen RMA")  method uses a kind of
reference file that summarizes information from many arrays, thus allowing
pre-processing of arrays using data from many chips without having to read
them all into memory.

There are frma data files available for commonly used human and
mouse arrays but none for ATH1/GPL198 so far as I can tell.

My question is:

Have you or anyone you know created an frma data file for the ATH1/GPL198
array? If yes, would you be willing to share it or maybe work together to
use it to process the ATH1 arrays from GEO?

Creating an frma is non-trivial, and the authors of the frma method
provide some ideas and advice on how to do it. Take-home message seems to
be that it's a good idea to include a sample of arrays from many
experiments. If you have suggestions or ideas on how to proceed I  would
be grateful for the advice.

Reference:
Thawing Frozen Robust Multi-array Analysis (fRMA)
http://www.biomedcentral.com/1471-2105/12/369

Best wishes,

Ann Loraine

-------------------------------
Ann Loraine, Ph.D.
Associate Professor
Department of Bioinformatics and Genomics
University of North Carolina at Charlotte
North Carolina Research Campus
600 Laureate Way
Kannapolis, NC 28081
704-250-5750
aloraine from uncc.edu
http://www.transvar.org
http://www.bioviz.org
http://www.uncc.edu




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