Bob MacCallum wrote: > Hello all, > > No it's not a new standard we have to adhere to (MIAD), I am wondering what is > the least amount of array design information I can give to BASE if I want to > load "hacked" data in from a non-supported platform (or from already processed > data) but still maintain the raw bioassay<->array design<->reporter links. > > I'm talking about making a fake array design with some made-up > position/coordinate data, and adding this to the "raw" data files. Sounds > nasty I know. > > What can I get away with, just "position" or "position + X + Y"? Given some > recent developments in the schema and no indications in the main > documentation, I would appreciate some guidance.
There are three options that are described by a FeatureIdentificationMethod object (see http://base.thep.lu.se/chrome/site/latest/api/net/sf/basedb/core/FeatureBatcher.html). The first option is to use coordinates, which can be either:[block, row, column] or [metaGridX, metaGridY, row, column]. I think this alternative is the least usable when "faking" an array design, but is the only alternative before BASE 2.6. The second option is to use position only. It must be an integer > 0. The position existed before BASE 2.6 but it was always assigned internally by BASE. With BASE 2.6 or later the position can be assigned by the import plug-in. The third option is to use a "featureId" which is a string value. This is completely new for BASE 2.6 and is the method used by the Illumina plug-ins package: http://baseplugins.thep.lu.se/wiki/net.sf.basedb.illumina In all three cases the given value(s) must be unique within an array design. There is a forth option to keep everything in files and not in the database, but if you want to do anything with that kind of data you'll need to write plug-ins that knows how to extract information from the files. This is the approach used with Affymetrix data (CEL and CDF files). /Nicklas ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
