Hi, As you describe it it seems like you have bead level data in your data files. The Illumina package for BASE expects bead summary data, i.e., the average for each bead type (together with some other numbers as described in http://baseplugins.thep.lu.se/browser/plugins/base2/net.sf.basedb.illumina/tags/1.2/README).
If the above is correct there are two ways forward: 1) Create a small program that converts bead level data to bead summary data. This could be in line with Markus' contribution on how to convert Illumina BeadStudio data to IBS, see http://baseplugins.thep.lu.se/browser/plugins/base2/net.sf.basedb.illumina/trunk/contrib/README_beadstudio2ibs.txt 2) Add support for reading bead level data files to the Illumina package, i.e., perform what a converter in bullet 1 above would do. A plug-in could do the averageing and store IBS like data in the database. This of course requires that Code colun in Lucas sample is the same as Illumicode in IBS files (the same requirement is also true for a converter in 1 above). I am not sure if 2) is something we want to see, we opted out from this earlier since the data files are really large. Also, we did not see any benefit on storing the bead level data. Of course, in our discussions we opted out because we did not want to store bead level data in the database, but we would not do that in this scenario (only store large files). Any thoughts? Jari luca.beltr...@unifi.it wrote: > Hello, > > I'm having trouble in creating bead summary files from bead level > files on BASE 2.9.2 using the Illumina plugin package version 1.2. > > I created the array designs, imported the features and the reporters. > Then I created a new raw bioassay and added two beadlevel files as > they were supplied to me. When activating the bead summary importer, I > get the following error (pasted from the log): > > Failed: Can't find start of data in file: File[id=386; > name=4449817059_A_1.txt] on line 101 in file 4449817059_A_1.txt > net.sf.basedb.core.BaseException: Can't find start of data in file: > File[id=386; name=4449817059_A_1.txt] on line 101 in file > 4449817059_A_1.txt > at > net.sf.basedb.illumina.plugins.BeadSummaryImporter.importScandata(BeadSummaryImporter.java:738) > at > net.sf.basedb.illumina.plugins.BeadSummaryImporter.run(BeadSummaryImporter.java:284) > at > net.sf.basedb.core.PluginExecutionRequest.invoke(PluginExecutionRequest.java:106) > at > net.sf.basedb.core.InternalJobQueue$JobRunner.run(InternalJobQueue.java:504) > at java.lang.Thread.run(Thread.java:619) > Caused by: net.sf.basedb.core.InvalidDataException: Can't find start > of data in file: File[id=386; name=4449817059_A_1.txt] > at > net.sf.basedb.illumina.plugins.BeadSummaryImporter.importScandata(BeadSummaryImporter.java:677) > ... 4 more > > I don't know why line 101, as it does not matter what it is on that > line (I made a backup of the bead level file and removed the offending > line just to make sure, since apparently setting "skip" as option in > case of errors has no effect). > > I noticed that the header in my bead level data is different than what > the README indicates, namely it is > > Code,Grn,GrnX,GrnY > > Also, the file is tab-separated, rather than comma-separated (but > substituting tabs to commas does not fix the problem). Is there a way > to work around this problem, is it a plugin limitation, or am I just > doing things in the wrong way? > > Thanks in advance. > > Please CC me in replies, I'm not subscribed to this list. > > > ------------------------------------------------------------------------------ > Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA > -OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise > -Strategies to boost innovation and cut costs with open source participation > -Receive a $600 discount off the registration fee with the source code: SFAD > http://p.sf.net/sfu/XcvMzF8H > _______________________________________________ > The BASE general discussion mailing list > basedb-users@lists.sourceforge.net > unsubscribe: send a mail with subject "unsubscribe" to > basedb-users-requ...@lists.sourceforge.net ------------------------------------------------------------------------------ Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA -OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise -Strategies to boost innovation and cut costs with open source participation -Receive a $600 discount off the registration fee with the source code: SFAD http://p.sf.net/sfu/XcvMzF8H _______________________________________________ The BASE general discussion mailing list basedb-users@lists.sourceforge.net unsubscribe: send a mail with subject "unsubscribe" to basedb-users-requ...@lists.sourceforge.net
