Make it possible for core analysis plug-ins to work on a subset of bioassays in a bioassayset

[Nicklas Nordborg]

Once ticket #685 is in place it should not be so difficult. The core plug-ins are:

• JEP extra value calculator
• JEP filter plug-in (already supports this but should be redone to use new methods in AbstractAnalysisPlugin?)
• JEP intensity transformer
• Base1PluginExecuter
• Lowess normalization
• Media ratio normalization

Depends on ticket#691

[Martin Svensson]

(In [3583]) References #686 Jep Formula Filter and JepExtraValueCalculator? can now work on subset of bioassays

[Martin Svensson]

(In [3584]) References #686 Updated gui contexts in JepExtraValueCalculator? to also include bioassays

[Martin Svensson]

(In [3587]) References #686 Two more coreplugins are updated AbstractAnalysisPlugin? got a method to set restriction on using selected bioassays

[Peter Johansson]

I may be ignorant, but why is this wanted? Is this a request from user community?

What is the use case? I cant see why a user would like to, e.g., lowess normalize a subset of bioassays (and keep the unnormalized data in the following analysis). Though I can see that people would like to select a subset of bioassays (e.g. those coming from patients of age below 55) and perform some analysis on that selected dataset. But wouldn't it be preferable to have one module creating the sub-BioAssaySet? and the AnalysisPlugin? doing the analysis. Otherwise, the golden rule is broken: "Each module should be responsible for one task and one task only."

If I am ignorant, please enlighten me.