[BioC] matrix transformation

Ido M. Tamir tamir at imp.ac.at
Mon Oct 18 12:50:02 CEST 2010

> Dear Mailing List,
> I wrote the following function "matrix2tuple.sf" to translate a "cartesian
> xy matrix" as a "tuple matrix", to store it in relational database. The
> code works fine for a test set. My problem is, my real matrix is 7000 x
> 10000 big, which ends up in 70'000'0000' tuples. Transformation takes days
> X(...
> Has anyone an idea, how I can optimize the described functions for speed?
> Best Wishes, Elmar Bucher

I didnt look at the R code, but the inserts could be sped up if you would
do it in batches and not individual inserts.

Something like:
100 x insert..

Maybe do a cheap profiling by just commenting out the db code to see
if the db is slowing it down.


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