Changeset 766


Ignore:
Timestamp:
Sep 16, 2008, 11:22:37 AM (13 years ago)
Author:
Jari Häkkinen
Message:

Addresses #129. Updated configuration files, reworked html result table generation, first version of README.

Location:
plugins/base1/se.lu.onk.ReplicateError/trunk
Files:
1 added
7 edited
2 copied
2 moved

Legend:

Unmodified
Added
Removed
  • plugins/base1/se.lu.onk.ReplicateError/trunk/build.xml

    r764 r766  
    100100     ================================= -->
    101101  <target name="package" depends="dist"
    102           description="--> Create a zip file for distribution.">
     102          description="--> Create a tgz file for distribution.">
    103103    <mkdir dir="${package}"/>
    104104    <mkdir dir="${package}/${basefilejar}"/>
  • plugins/base1/se.lu.onk.ReplicateError/trunk/lib/AAindex.html

    • Property svn:keywords set to Id
    r758 r766  
    11<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Frameset//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-frameset.dtd">
     2
     3<!-- $Id$ -->
     4
    25<html>
    36<head>
    47<meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1" />
    5 <title>BASE 1.2.16dev - Experiment Enell:Enell Plugin</title>
     8<title>ReplicateError (across assays)</title>
    69</head>
    710<frameset rows="100px,*" border="0">
  • plugins/base1/se.lu.onk.ReplicateError/trunk/lib/AAtabs.html

    • Property svn:keywords set to Id
    r758 r766  
    11<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Frameset//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-frameset.dtd">
     2
     3<!-- $Id$ -->
     4
    25<html>
    36<head>
     
    69<body>
    710<table cellpadding=1 cellspacing=2 border=0>
    8 <tr><th colspan=3 class=pagehead>ReplicateError: results</th></tr>
     11<tr><th colspan=3 class=pagehead>ReplicateError (across assays) results:</th></tr>
     12
     13<!--
     14If you use this plug-in in BASE 1.2 you may want to enable the next line:
     15
    916<tr><td colspan=3><a class="large" target="bmain" href="../../../../experiment_edit.phtml?i_e=-1&amp;location=experiment_list.phtml">Return</a></td></tr>
     17-->
    1018
    1119<tr>
  • plugins/base1/se.lu.onk.ReplicateError/trunk/lib/README.old

    • Property svn:keywords set to Id
  • plugins/base1/se.lu.onk.ReplicateError/trunk/lib/WAindex.html

    • Property svn:keywords set to Id
    r758 r766  
    11<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Frameset//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-frameset.dtd">
     2
     3<!-- $Id$ -->
     4
    25<html>
    36<head>
    47<meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1" />
    5 <title>BASE 1.2.16dev - Experiment Enell:Enell Plugin</title>
     8<title>ReplicateError (within assays)</title>
    69</head>
    710<frameset rows="100px,*" border="0">
  • plugins/base1/se.lu.onk.ReplicateError/trunk/lib/WAtabs.html

    • Property svn:keywords set to Id
    r758 r766  
    11<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Frameset//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-frameset.dtd">
     2
     3<!-- $Id$ -->
     4
    25<html>
    36<head>
     
    69<body>
    710<table cellpadding=1 cellspacing=2 border=0>
    8 <tr><th colspan=3 class=pagehead>ReplicateError: results</th></tr>
     11<tr><th colspan=3 class=pagehead>ReplicateError (within assays) results:</th></tr>
     12
     13<!--
     14If you use this plug-in in BASE 1.2 you may want to enable the next line:
     15
    916<tr><td colspan=3><a class="large" target="bmain" href="../../../../experiment_edit.phtml?i_e=-1&amp;location=experiment_list.phtml">Return</a></td></tr>
     17-->
    1018
    1119<tr>
  • plugins/base1/se.lu.onk.ReplicateError/trunk/lib/base.css

    • Property svn:keywords set to Id
    r758 r766  
     1<!-- $Id$ -->
     2
    13a:active { text-decoration: none; color: #ff5050; }
    24a:link { text-decoration: none; color: #1000d0; }
  • plugins/base1/se.lu.onk.ReplicateError/trunk/lib/pluginConfigurationAA.base

    r149 r766  
    22section plugin
    33uniqueName  onk.lu.se/enell/ReplicateError
    4 versionNumber 1.1
     4versionNumber 1.3
    55name  Filter: ReplicateError (across assays)
    66descr Implementation of 'Analysis of replicates' (page 8) (Fig4b page 6)\r\nWithin the fold: assessing differential expression measures and reproducibility in microarray assays.\r\nYang IV et al. Genome Biol. 2002 Oct 24;3(11):research0062. Epub 2002 Oct 24.
     
    2020%
    21211 h section   30  settings    0
    22 2 f sdLimit Standard deviation limit  30  2.0   0
    23 3 e center  Center of mass  30  0 0\tmedian\t1\tmean  0
    24 4 t assayname Assayname 10  %   0
    25 5 t group Group 10  1   0
    26 6 t sort  Sort  10      0
    27 7 e leaveSingletons Leave singletons  30  false true\tyes\tfalse\tno  0
    28 8 t includeassays Include assays  30    0
     222 e strictReplicate Replicate filter  30  true  true\ton\tfalse\toff  1
     233 f sdLimit Standard deviation limit  30  2.0   0
     244 e newBAS  Create new bioassay set 30  true  true\tyes\tfalse\tno  1
     255 e leaveSingletons Leave singletons  30  false true\tyes\tfalse\tno  0
     266 e leaveDataFiles  Put gnuplot file in zip archive 30  false true\tyes\tfalse\tno  1
     277 t assayname assayname 10  %   0
     288 t group Group 10  1   0
     299 t sort  Sort  10      0
     3010  e center  Center of mass  30  0 0\tmedian\t1\tmean  0
     3111  t sort  Sort  30      1
     3212  t includeassays Assays to include 30      0
  • plugins/base1/se.lu.onk.ReplicateError/trunk/lib/pluginConfigurationWA.base

    r149 r766  
    22section plugin
    33uniqueName  onk.lu.se/enell/ReplicateError
    4 versionNumber 1.1
     4versionNumber 1.3
    55name  Filter: ReplicateError (within assays)
    6 descr Implementation of 'Analysis of replicates' (page 8) (Fig4b page 6)\r\nWithin the fold: assessing differential expression measures and reproducibility in microarray assays.\r\nYang IV et al. Genome Biol. 2002 Oct 24;3(11):research0062. Epub 2002 Oct 24.
     6descr Implementation of 'Analysis of replicates'\r\nWithin the fold: assessing differential expression measures and reproducibility in microarray assays.\r\nYang IV et al. Genome Biol. 2002 Oct 24;3(11):research0062. Epub 2002 Oct 24.
    77execName  runWA
    88geneAverages  0
     
    1919columns position  valueType name  commonName  options defaultValue  enumOptions removed
    2020%
    21 1 h section   30  settings    0
    22 2 f sdLimit Standard deviation limit  30  2.0   0
    23 3 e center  Center of mass  30  0 0\tmedian\t1\tmean  0
    24 4 e leaveSingletons Leave singletons  30  false true\tyes\tfalse\tno  0
     211 e strictReplicate Replicate filter  30  true  true\ton\tfalse\toff  1
     222 h section   30  settings    0
     233 f sdLimit Standard deviation limit  30  2.0   0
     244 e newBAS  Create new bioassay set 30  true  true\tyes\tfalse\tno  1
     255 e leaveSingletons Leave singletons  30  false true\tyes\tfalse\tno  0
     266 e leaveDataFiles  Put gnuplot file in zip archive 30  false true\tyes\tfalse\tno  1
     277 e method  Method  30  1 1\tSD Limit\t2\tmin(ch1, ch2)\t3\t### 1
     288 f startvalue  Start value 30      1
     299 f stepSize  Step size 30      1
     3010  f rTarget R target  30  0.95    1
     3111  e center  Center of mass  30  0 0\tMedian\t1\tMean  0
    2532
  • plugins/base1/se.lu.onk.ReplicateError/trunk/lib/runAA

    • Property svn:executable set to *
    • Property svn:keywords set to Id
    r149 r766  
    11#!/bin/bash -
    22
     3# $Id$
     4
    35progdir="`dirname \"$0\"`"
    4 java -cp "$CLASSPATH:$progdir/ReplicateError.jar" replicateerror.ReplicateError -aa
     6
     7java -Xmx512M -cp "$CLASSPATH:$progdir/BaseFile/BaseFile.jar:$progdir/ReplicateError.jar" replicateerror.ReplicateError -aa
    58R --no-save --slave < plot.R > R.out
    6 cp $progdir/index.html .
     9cp $progdir/AAindex.html index.html
    710cp $progdir/base.css data/
    8 cp $progdir/tabs.html data/
     11cp $progdir/AAtabs.html data/tabs.html
    912rm -f data/*.data
  • plugins/base1/se.lu.onk.ReplicateError/trunk/lib/runWA

    • Property svn:executable set to *
    • Property svn:keywords set to Id
    r149 r766  
    11#!/bin/bash -
    22
     3# $Id$
     4
    35progdir="`dirname \"$0\"`"
    4 java -cp "$CLASSPATH:$progdir/ReplicateError.jar" replicateerror.ReplicateError -wa
     6
     7java -Xmx512M -cp "$CLASSPATH:$progdir/BaseFile/BaseFile.jar:$progdir/ReplicateError.jar" replicateerror.ReplicateError -wa
    58R --no-save --slave < plot.R > R.out
    6 cp $progdir/index.html .
     9cp $progdir/WAindex.html index.html
    710cp $progdir/base.css data/
    8 cp $progdir/tabs.html data/
     11cp $progdir/WAtabs.html data/tabs.html
    912rm -f data/*.data
Note: See TracChangeset for help on using the changeset viewer.