Opened 13 years ago

Closed 12 years ago

#118 closed task (fixed)

Create qQuantile normalizer (aka cubic-spline normalizer)

Reported by: Jari Häkkinen Owned by: Jari Häkkinen
Priority: major Milestone: 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 (27)

comment:1 Changed 13 years ago by Martin Svensson

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

comment:2 Changed 13 years ago by Martin Svensson

Status: new → assigned

comment:3 Changed 13 years ago by Jari Häkkinen

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 Changed 13 years ago by Jari Häkkinen

Status: new → assigned

comment:5 Changed 13 years ago by Jari Häkkinen

Description: modified (diff)

comment:6 Changed 12 years ago by Jari Häkkinen

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

comment:7 Changed 12 years ago by Jari Häkkinen

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

comment:8 Changed 12 years ago by Jari Häkkinen

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

comment:9 Changed 12 years ago by Jari Häkkinen

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

comment:10 Changed 12 years ago by Jari Häkkinen

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

comment:11 Changed 12 years ago by Jari Häkkinen

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

comment:12 Changed 12 years ago by Jari Häkkinen

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

comment:13 Changed 12 years ago by Jari Häkkinen

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

comment:14 Changed 12 years ago by Jari Häkkinen

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

comment:15 Changed 12 years ago by Jari Häkkinen

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

comment:16 Changed 12 years ago by Jari Häkkinen

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

comment:17 Changed 12 years ago by Jari Häkkinen

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

comment:18 Changed 12 years ago by Jari Häkkinen

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

comment:19 Changed 12 years ago by Jari Häkkinen

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

comment:20 Changed 12 years ago by Jari Häkkinen

(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 Changed 12 years ago by Jari Häkkinen

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

comment:22 Changed 12 years ago by Jari Häkkinen

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

comment:23 Changed 12 years ago by Jari Häkkinen

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

comment:24 Changed 12 years ago by Jari Häkkinen

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

comment:25 Changed 12 years ago by Jari Häkkinen

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

comment:26 Changed 12 years ago by Jari Häkkinen

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

comment:27 Changed 12 years ago by Jari Häkkinen

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

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