> Thanks Nicklas for the help with boolean queries. Now I'm confused by
> something else also affy-related.
>
> I'm trying to write code to lookup which ArrayDesigns a Reporter is on.
> For non-Affy arrays this is easy (join via arrayDesignBlocks, features and
> reporter).
>
> For Affy arrays it looks like we have to use the CDF file through the Affy API
> - get all the reporter ids (e.g. ProbeSetNames) and put them in a hash for
> reverse lookup later.
>
> Here's a code snippet to do some of that (see last email for the definition of
> affyQuery). A lot of the code is taken directly from
> net/sf/basedb/core/Affymetrix.java, which is used by the "Affymetrix CDF
> probeset importer" plugin for Affy array design (see the "verify reporters"
> link on any Affy ArrayDesign page). When I run this plugin as the same user
> who runs the code below, it works fine. However I get a NullPointerException
> with my code...
>
The Affymetrix.loadCdfFile() method only parses the headers. You must
call cdf.clear() and cdf.read() to parse the entire file.
I have found that the Fusion SDK is unfortunately not very informative
when it comes to error messages and doesn't have much of error handling
either.
> Hashtable affyProbeLookup = new Hashtable();
>
> ItemResultList<ArrayDesign> affyList = affyQuery.list(dc);
> for (ArrayDesign ad : affyList) {
> int adId = ad.getId();
> FusionCDFData cdf = Affymetrix.loadCdfFile(Affymetrix.getCdfFile(ad));
> if (cdf == null) continue;
> int numProbesets = cdf.getHeader().getNumProbeSets();
> int index = 0;
> while (index < numProbesets) {
> String probesetId = cdf.getProbeSetName(index); // Line 96
> affyProbeLookup.put(probesetId, adId);
> index++;
> }
> }
>
> Exception in thread "main" java.lang.NullPointerException
> at affymetrix.gcos.cdf.CDFFileData.getProbeSetName(Unknown Source)
> at affymetrix.fusion.cdf.FusionCDFData.getProbeSetName(Unknown Source)
> at base_api_test.run_test(base_api_test.java:96)
> at base_api_test.main(base_api_test.java:216)
>
>
> note: the cdf object seems OK (numProbesets is set properly).
>
>
> If anyone can point me in the right direction, it would be appreciated.
> It's a bit difficult not having the Affy source and line numbers
> (is that available?)
You'll have to ask Affymetrix for that. It all depends on how the
package was compiled.
I also have to mention that the 2.5 release will have a lot of changes
in how Affymetrix data is handled.
First, the special case used for Affymetrix has been replaced with a
more generic way to support file attachements to any raw data types.
Most of the methods in the Affymetrix class have been deprecated and
replaced with something else (there are hints in the javadoc).
Second, BASE 2.5 will store CEL, CDF and other large files in a
compressed format. To avoid having to unpack and copy the CEL and CDF
files each time we just want to read the first 10-20 header lines BASE
2.5 will ship with a modified version of the Fusion SDK. The
modifications have made it possible to pass a java.io.InputStream to the
Fusion SDK instead of filenames (java.io.File). This may make it behave
a bit differently than it did before. We have only modified the parts
that we are using in BASE. Other parts have been left as they are. If
you are only doing similar things as we do in the Affymetrix.java class
it should be safe. The modified Fusion SDK can be found on
http://trac.thep.lu.se/trac/basehacks
/Nicklas
-------------------------------------------------------------------------
This SF.net email is sponsored by: Splunk Inc.
Still grepping through log files to find problems? Stop.
Now Search log events and configuration files using AJAX and a browser.
Download your FREE copy of Splunk now >> http://get.splunk.com/
_______________________________________________
basedb-devel mailing list
basedb-devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/basedb-devel
