Opened 16 years ago

Closed 16 years ago

Last modified 3 years ago

#118 closed task (fixed)

Create qQuantile normalizer (aka cubic-spline normalizer)

Reported by: Jari Häkkinen Owned by: Jari Häkkinen
Priority: major Milestone: ZZ Normalization package v1.1
Component: net.sf.basedb.normalizers Keywords:
Cc:

Description (last modified by Jari Häkkinen)

This normalizer is based on the work of Workman et al., ​http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=12225587

Change History (28)

comment:1 by Martin Svensson, 16 years ago

Component: net.sf.basedb.examples.extensions → net.sf.basedb.normalizations
Milestone: ZZ Other tickets → Normalization package

comment:2 by Martin Svensson, 16 years ago

Status: new → assigned

comment:3 by Jari Häkkinen, 16 years ago

Owner: changed from Martin Svensson to Jari Häkkinen
Status: assigned → new

This normalizer is based on the work of Workman et al., ​http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=12225587

comment:4 by Jari Häkkinen, 16 years ago

Status: new → assigned

comment:5 by Jari Häkkinen, 16 years ago

Description: modified (diff)

comment:6 by Jari Häkkinen, 16 years ago

Summary: Create cubic-spline normalizer → Create qQuantil normalizer (aka cubic-spline normalizer)

comment:7 by Jari Häkkinen, 16 years ago

Summary: Create qQuantil normalizer (aka cubic-spline normalizer) → Create qQuantile normalizer (aka cubic-spline normalizer)

comment:8 by Jari Häkkinen, 16 years ago

(In [952]) Addresses #118. Added underlying C++ binary for the qQuantile.

comment:9 by Jari Häkkinen, 16 years ago

(In [953]) Refs #118. Changes suggested by the yat developer team.

comment:10 by Jari Häkkinen, 16 years ago

(In [954]) Refs #118. Changes suggested by the yat developer team.

comment:11 by Jari Häkkinen, 16 years ago

(In [955]) Refs #118. Changes suggested by the yat developer team.

comment:12 by Jari Häkkinen, 16 years ago

(In [960]) Refs #118. Changes suggested by the yat developer team.

comment:13 by Jari Häkkinen, 16 years ago

(In [961]) Refs #118 and #161. PluginUtilities download support. Added distclean ant target.

comment:14 by Jari Häkkinen, 16 years ago

(In [972]) Addresses #118. Load of java wrapper works but manual install of plug-in required.

comment:15 by Jari Häkkinen, 16 years ago

(In [973]) Addresses #118. Required yat version is 0.5 or later

comment:16 by Jari Häkkinen, 16 years ago

(In [993]) Addresses #118. First version of working qQuantileNormalizer.

comment:17 by Jari Häkkinen, 16 years ago

(In [998]) Addresses #118 and #183. Moved export of data to an export method.

comment:18 by Jari Häkkinen, 16 years ago

(In [1020]) Addresses #118 and fixes #187.

comment:19 by Jari Häkkinen, 16 years ago

(In [1043]) Addresses #118 and #206. This code produces the same result as the preivous code but fails miserably with missing values.

comment:20 by Jari Häkkinen, 16 years ago

(In [1044]) Addresses #118 and #206. If no assay data is given use the average of all assays as reference ... fixed create_target for this case.

comment:21 by Jari Häkkinen, 16 years ago

(In [1050]) Addresses #118. Non-logged input values are expected, geometric mean is used for averaging.

comment:22 by Jari Häkkinen, 16 years ago

(In [1062]) Addresses #118. Added support to use either mean or median in target calculation.

comment:23 by Jari Häkkinen, 16 years ago

(In [1064]) Addresses #118. Calculate target with median instead of mean.

comment:24 by Jari Häkkinen, 16 years ago

(In [1067]) Addresses #118. Forcing negative and 0 intensities to be NaNs with 0 weight.

comment:25 by Jari Häkkinen, 16 years ago

(In [1073]) Addresses #118. q=max(10,min(100,target_size/10))

comment:26 by Jari Häkkinen, 16 years ago

(In [1074]) Addresses #118. Added documentation for qQuantiler.

comment:27 by Jari Häkkinen, 16 years ago

Resolution: → fixed
Status: assigned → closed

(In [1079]) Fixes #118. qQuantiler will only show up in proper context and normalizers are now dependent on PluginUtilities-0.2

comment:28 by Nicklas Nordborg, 3 years ago

Milestone: Normalization package v1.1 → ZZ Normalization package v1.1

Milestone renamed

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