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
