Collett, James R skrev: > 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). >
We are aware of the shortcomings of the current plug-in. Unfortunately, we currently have no time to extend and improve it. Another reason that further slows down the progress is that we do not use the Affymetrix platform ourselves. There are many improvements that could be done as you point out. There are users who extend the affymetrix plug-in but these additions have not become public yet and I am not sure if they will be published. > 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. It should probably be straightforward to add more functionality to the plug-in using the different Affymetrix tools. In the simple case one would just add an option for the user to select which tool to use, and a more fancy way would be that the plug-in checks which tools are appropriate for the data at hand. > 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? This is a great idea! The different apt tools should be in one single package. This will make Affymetrix usage simpler for BASE users (and the administrators). So, we are happy to work with you on improving the plugin. The first steps forward. You already have read access to the source code for the plug-in through http://baseplugins.thep.lu.se/wiki/se.lu.thep.affymetrix Read the instructions on this page on how to check-out the latest development code. > Thanks, and Congratulations on BASE 2.5.0 - it's been working > exceedingly well for us! Thank you, Jari > 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
