On 2010-04-14 15:06, Gerrit Botha wrote: > Dear Base users, > > I am unable to import reporters from an Affymetrix unsupported Exon > Array CDF (e.g. unsupported Mouse 1.0 ST Exon Array) with the Affymetrix > CDF probeset importer. The job fails with error " > java.lang.ArrayIndexOutOfBoundsException". I suspect that the CDF is not > in the exact CDF standard and therefor BASE has trouble reading the > file. Is there any way around this? I need to do some RMAExpress > analysis so would need to have those missing reporters.
I don't know much about the various Affymetrix formats. The Affymetrix support that is currently in BASE was developed with the help of external contributions which also provided us with access to test data sets. The code is based on/uses a rather old version of a development kit provided by Affymetrix (Fusion SDK 1.0.9). Since we are not using Affymetrix ourselves we have not kept this up to date with new releases from Affymetrix (the latest seems to be 1.1.0). The CDF files we have worked with are plain text files and all start with: [CDF] Version=GC3.0 If your files are different maybe you can convert them to the older format? Otherwise the only other option is to fix the BASE code so that it works with the newer Fusion SDK. There is already a ticket about this in our trac system (http://base.thep.lu.se/ticket/1402) but we would really need help implementing this. By the way, can you post the complete stacktrace? /Nicklas ------------------------------------------------------------------------------ Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev _______________________________________________ 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
