Opened 15 years ago

Closed 15 years ago

#686 closed enhancement (wontfix)

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

Reported by: Nicklas Nordborg Owned by: Martin Svensson
Priority: minor Milestone: BASE 2.4
Component: coreplugins Version:
Keywords: Cc:

Description (last modified by Martin Svensson)

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

Change History (8)

comment:1 Changed 15 years ago by Martin Svensson

Owner: changed from everyone to Martin Svensson
Status: newassigned

comment:2 Changed 15 years ago by Martin Svensson

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

comment:3 Changed 15 years ago by Martin Svensson

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

comment:4 Changed 15 years ago by Martin Svensson

Description: modified (diff)

comment:5 Changed 15 years ago by Martin Svensson

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

comment:6 Changed 15 years ago by 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.

comment:7 Changed 15 years ago by Nicklas Nordborg

Component: webcoreplugins

comment:8 Changed 15 years ago by Jari Häkkinen

Resolution: wontfix
Status: assignedclosed
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