Opened 11 years ago

Closed 11 years ago

Last modified 11 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 11 years ago by jari

Description: modified (diff)
Owner: changed from everyone to jari
Status: newassigned

comment:2 Changed 11 years ago by jari

Resolution: fixed
Status: assignedclosed

(In [4360]) Fixes #1077.

comment:3 Changed 11 years ago by Nicklas Nordborg

(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 11 years ago by jari

Further issues found, reopening this ticket.

comment:5 Changed 11 years ago by jari

Resolution: fixed
Status: closedreopened

comment:6 Changed 11 years ago by jari

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

comment:7 Changed 11 years ago by Nicklas Nordborg

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

Added warning in update documentation.

comment:8 Changed 11 years ago by jari

Resolution: fixed
Status: reopenedclosed

(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 11 years ago by Nicklas Nordborg

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

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

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