Micha Bayer wrote: > Hi, > > Is there a way of programmatically storing externally normalized > microarray data in BASE? I have been looking through the API but can't > seem to find an obvious way of doing this. > > We run a workflow outside BASE (currently in GenePattern) which pulls > data out of BASE (using the BASE client API) and then normalizes it > using an R script that calls Bioconductor functions. I then need to > store that normalized data back into BASE so it can be reused later, > rather than having to do the lengthy normalization again. > > Is there a way of creating BioAssaySet objects directly and importing > the external data into it? And do I need to create a root BioAssaySet > first? I am kind of out of my depth here...... :-)
Yes, it is possible to do this the same way as, for example, the existing Lowess normalization plug-in does it. This is the general outline: 1. Call BioassaySet.newTransformation() to create a new transformation item. Give it a meaningful name and description, e.g. "GenePattern normalization using XXX method...." 2. Call Transformation.newProduct() to create the child bioassayset that stores the normalized data. Give it also a meaningful name and description. 3. Call BioassaySet.getSpotBatcher() to create a SpotBatcher object. Use the insert() method to store the normalized intensities. The above procedure can be used when you already have a (root) bioassayset with your data. If you start out with raw data you must create a root bioassayset. In this case, you should call Experiment.newTransformation() to create the transformation in the first step. In step 3 you may also have to do: BioAssaySet.getPositionBatcher() which is used to assign reporters to the normalized data, and BioAssaySet.getMappingBatcher() if you need to keep links to the raw data. I don't know if this made things clearer for you. There is also some information available at http://base.thep.lu.se/chrome/site/doc/development/overview/dynamic/index.html The document is rather old and I can't say if it is correct in all details. You can also check the code for the RMAExpress plug-in athttp://lev.thep.lu.se/trac/baseplugins/wiki/se.lu.thep.affymetrix which also uses an external program (RMAExpress) for normalization of Affymetrix data. /Nicklas ------------------------------------------------------------------------- This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to [EMAIL PROTECTED]
