A check for reporter information is needed when adding/using affymetrix data

[Jari Häkkinen]

Affymetrix data can be used up to the point when a plug-in (RMAExpress) tries to push results into the dynamic tables. At this point the core will throw an exception complaining about missing reporters. The behaviour is assymetric compared to genepix where import of raw bioassays cannot be done if no reporter information is available in the database.

For Affymetrix a similar check should be done, either when creating new raw bioassays or before starting plug-ins.

[Jari Häkkinen]

Relates to ticket:372

[Nicklas Nordborg]

The check would probably have to be done when creating the array design since it is the CDF file that has information about the reporters. The CEL file just contains references to the CDF file. There is a LGPL java package at ​http://morden.csee.usf.edu/software/ for parsing CDF files in both text and XDA format.

However, checking that the reporters exists when creating the array design is not a guarantee that the reporter will exist when doing the RMAExpress normalisation. There is nothing that prevents that the reporters are deleted in the mean time. In other words, the RMAExpress plugin should never expect that the reporters exists.

[Jari Häkkinen]

Milestone BASE 2.4 deleted

[Nicklas Nordborg]

(In [3482]) Fixes #435.