Nicklas Nordborg wrote: > 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 > > The CDF I have download is in ASCII format and is of version GC3.0 (http://www.affymetrix.com/Auth/support/downloads/library_files/MoEx-1_0-st-v1.text.cdf.zip). I believe the way it was created is insufficient for BASE to load. On aroma-project.org I found CDF files generated for the same chip. I will try to load this otherwise create my own version.
The alternative option would be to write a BASE plugin for for importing probesets using exon library data (CLF and PGF files). This would probably be more tricky. The stack trace was only "java.lang.ArrayIndexOutOfBoundsException". This is not really informative so is there any other place except in the database itself where more information is provided. Thanks for the advice. ------------------------------------------------------------------------------ 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
