Hi,The current implementation of the affymetrix plugin Plier.java relies on the Affymetrix Power Tools binary apt-probeset.summarize (analysis option plier-mm) . However, none of the other options in apt-probeset- summarize are made available for the user.
I have created a new plugin called APT Summarize that extends Plier.java with other options of transformations, PM intensity adjustments and quantifications. Th plugin relies on AbstractExternalBinaryPlugin.
Are you interested in me sharing the plugin with the BASE community? If yes, how do I proceed? Can I add the plugin to a new branch of (plug-ins) se.lu.thep.affymetrix?
Best, Robin Andersson --- Robin Andersson, PhD student Linnaeus Centre for Bioinformatics Uppsala University BMC, Box 598, SE-751 24 Uppsala, Sweden phone: +46 18 471 66 86 (admin: 66 90) fax: +46 18 471 66 98 office: BMC, C6:315a email: [EMAIL PROTECTED] http://www.lcb.uu.se/~robina/
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