Opened 10 years ago

Closed 10 years ago

Last modified 10 years ago

#1077 closed defect (fixed)

Lowess normalization broken

Reported by: jari Owned by: jari
Priority: blocker Milestone: BASE 2.7.2
Component: coreplugins Version:
Keywords: Cc:

Description (last modified by jari)

This problem affects all versions of BASE2.

As pointed out in the BASE users mailing list (http://www.mail-archive.com/basedb-users@lists.sourceforge.net/msg01478.html) there is a flaw in the lowess plug-in shipped with BASE. Users using the original BASE1 distributed lowess plug-in with the Base1PluginExecuter wrapper are not affected.

The fix is a simple one line change but affects all bioassays normalized with lowess and consequently all analysis following a lowess normalization must be redone. The changes to be expected to analysis results varies with raw data quality, where good quality raw data will have little effect from the miscalculation in the lowess plug-in.

Change History (9)

comment:1 Changed 10 years ago by jari

  • Description modified (diff)
  • Owner changed from everyone to jari
  • Status changed from new to assigned

comment:2 Changed 10 years ago by jari

  • Resolution set to fixed
  • Status changed from assigned to closed

(In [4360]) Fixes #1077.

comment:3 Changed 10 years ago by nicklas

(In [4361]) References #1077: Lowess normalization broken

Added script for finding and tagging experiments/bioassay sets that are affected by this bug. Need to document this in the installation/update documentation. Basically it works like this:

cd <base_dir>/bin
./onetimefix.sh lowess_warn -u root -p root_password -f

This will find and display all experiments/bioassay sets that have used the LOWESS plug-in. The -f flag causes those experiements/bioassay sets to be tagged with FIX LOWESS.

comment:4 Changed 10 years ago by jari

Further issues found, reopening this ticket.

comment:5 Changed 10 years ago by jari

  • Resolution fixed deleted
  • Status changed from closed to reopened

comment:6 Changed 10 years ago by jari

(In [4363]) Addresses #1077. A couple of more issues found. Further quality control needed before release.

comment:7 Changed 10 years ago by nicklas

(In [4364]) References #1077: Lowess normalization broken

Added warning in update documentation.

comment:8 Changed 10 years ago by jari

  • Resolution set to fixed
  • Status changed from reopened to closed

(In [4367]) Fixes #1077. Changed help text on step parameter, also changed default value for the parameter. The default now corresponds to the BASE1 default.

comment:9 Changed 10 years ago by nicklas

(In [4445]) References #1077: Lowess normalization broken

Updated images in "roles" test document with correctly normalized ones.

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