Opened 17 years ago

Closed 17 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 by Martin Svensson, 17 years ago

Owner: changed from everyone to Martin Svensson
Status: newassigned

comment:2 by Martin Svensson, 17 years ago

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

comment:3 by Martin Svensson, 17 years ago

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

comment:4 by Martin Svensson, 17 years ago

Description: modified (diff)

comment:5 by Martin Svensson, 17 years ago

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

comment:6 by Peter Johansson, 17 years ago

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 by Nicklas Nordborg, 17 years ago

Component: webcoreplugins

comment:8 by Jari Häkkinen, 17 years ago

Resolution: wontfix
Status: assignedclosed
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