[Bioperl-microarray] SOFT parsers

Sean Davis sdavis2 at mail.nih.gov
Thu Dec 28 05:15:25 UTC 2006

Michael Muratet US-Huntsville wrote:
> Greetings
> There was a thread a few years ago regarding parsers for SOFT-formatted
> data (the format used by the NCBI/GEO database). Has anybody ever
> developed one that would put the data into a database or into another
> format? 
Hi, Michael.  I have not written anything for perl, but I am the author 
of the GEOquery package for the R/Bioconductor project 
(http://www.bioconductor.org).  It can download and parse all of the 
SOFT format files (sample, platform, series, and dataset) into objects 
in R.  Once in R, you can apply pretty much any analysis method for 
microarray data, as most of these methods are available as Bioconductor 

I am in the process of converting GEOquery to use the MINiML format 
files (XML) instead of the SOFT format.  If you decide that you need to 
use perl, I would highly suggest that you use the MINiML format files 
instead of SOFT.

Hope that helps.


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