Jim, I have been working a while building plugins for the apt-probeset- summarize and apt-probeset-genotype command line tools. These two plugins implement the AbstractExternalBinaryPlugin in affymetrix.jar.
Some additional testing is needed before I release the package for the BASE community. I haven't tried the apt-cel-extract tool yet but understand the usefulness of such a plugin if raw data need to be deposited in the database prior to further analyses. In contrast to the Plier plugin that just do the plier-mm analysis (using apt-probeset-summarize), I have made all possible analysis parameters to these tools available in the plugins. Perhaps you can reuse some of the code in these plugins. I will let you know when the code is ready for release. /Robin On Jan 2, 2008, at 2:27 AM, Collett, James R wrote: > Happy New Year, BASErs! > > We are developing metagenomic assays using Affy chips with > custom-designed probe sets. The tools available for analyzing standard > Affy gene expression data using pm-mm comparisons, however, are not > relevant to our chip design and analytical approach (we're only > using pm > probes). > > Accordingly, we would like to adapt the BASE affymetrix.jar plugin to > use other executables in the Affymetrix Power Tools suite besides just > the apt-probeset-summarize. Specifically, we would like to use > apt-cel-extract within affymetrix.jar to simply extract feature > intensities, probe IDs, probe set IDs, and XY coordinates from CEL > files > into new root bioassay sets. I have already used apt-cel-extract > on the > command line to successfully extract these fields from CEL files into > text files. > > For now, simply trying to feed our CEL files into the current Affy > PLIER > plugin within BASE 2.5.0 gives (not surprisingly) the following error: > > java.io.IOException: Unexpected exit of PLIER sub-process. Return > value: > 1 > at se.lu.thep.affymetrix.Plier.runBinary(Plier.java:157) > at > se.lu.thep.affymetrix.AbstractExternalBinaryPlugin.run > (AbstractExternalB > inaryPlugin.java:262) > at > net.sf.basedb.core.PluginExecutionRequest.invoke > (PluginExecutionRequest. > java:89) > at > net.sf.basedb.core.InternalJobQueue$JobRunner.run > (InternalJobQueue.java: > 435) > at java.lang.Thread.run(Thread.java:619) > > Are any of you interested in working with us to expand > affymetrix.jar to > include functionalities from apt-cel-extract and perhaps others in the > the Affy Power Tools suite? If not, can you give us some > suggestions on > how we might best get started on this, and what kinds of challenges or > incompatibilities that we might face? > > Thanks, and Congratulations on BASE 2.5.0 - it's been working > exceedingly well for us! > > Jim Collett > > James R. Collett, Ph.D. > Systems Biology Fellow > Chemical and Biological Process Development Group > Pacific Northwest National Laboratory > > > > > > > > > > > > ---------------------------------------------------------------------- > --- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2005. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > basedb-devel mailing list > basedb-devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/basedb-devel --- 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/ ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ basedb-devel mailing list basedb-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/basedb-devel
