Changeset 1032


Ignore:
Timestamp:
Apr 7, 2009, 8:24:34 AM (14 years ago)
Author:
Nicklas Nordborg
Message:

Fixes #202: Change source files to UTF-8

Location:
plugins/base2/net.sf.basedb.illumina/trunk
Files:
5 edited

Legend:

Unmodified
Added
Removed

  • plugins/base2/net.sf.basedb.illumina/trunk/README

    r941 r1032  
    2929 
    3030 2. Illumina Bead Summary (IBS) files. The IBS files contain quantified probe intensities.
    31  3. Illumina Sentrix® Array binary manifest (BGX) file. The BGX files contain probe annotations.
     31 3. Illumina Sentrix Array binary manifest (BGX) file. The BGX files contain probe annotations.
    3232 
    3333For SNP experiments:
    … …  
    4646
    4747The Illumina BeadArray Reader is a scanner that can read arrays including Illumina
    48 Sentrix® BeadChips and Sentrix® Array Matrices (SAMs). Operation of the BeadArray
    49 Reader and image aquisition from Sentrix® arrays is handled by the Illumina BeadScan
     48Sentrix BeadChips and Sentrix Array Matrices (SAMs). Operation of the BeadArray
     49Reader and image aquisition from Sentrix arrays is handled by the Illumina BeadScan
    5050software.
    5151
    … …  
    5454as the Illumina BeadStudio software.
    5555
    56 The Illumina plug-ins package for BASE reads Illumina Sentrix® Array data from
     56The Illumina plug-ins package for BASE reads Illumina Sentrix Array data from
    5757Illumina Bead Summary (IBS) files. The IBS files are not by default outputted by
    5858the BeadArray Reader and the scanner must be configured to do so. Once the
    … …  
    6161to contact their local Illumina Field Application Scientist.
    6262
    63 The IBS files are text files that contain bead-type level data for scanned Sentrix®
     63The IBS files are text files that contain bead-type level data for scanned Sentrix
    6464arrays. The file format is explained in detail in the section Illumina Bead Summary
    6565files.
    … …  
    6767== Illumina Bead Summary (IBS) files ==
    6868
    69 The IBS files contain bead-type level data for scanned Sentrix® arrays.
     69The IBS files contain bead-type level data for scanned Sentrix arrays.
    7070The IBS files are simple comma separated text files with file extension .csv.
    7171The IBS files are outputted by the BeadArray Reader in the same directory as any
    … …  
    8585The column content in an IBS file is described below.
    8686 - ''' Illumicode ''': A code corresponding to the Array_Address_Id in the
    87  Illumina Sentrix® Array binary manifest (BGX) file. Note that the Illuminacode is a string (or integer) of varying length. The Array_Address_Id is a string with a fixed lenght of 10 characters that consists of an Illuminacode padded with zeros.
     87 Illumina Sentrix Array binary manifest (BGX) file. Note that the Illuminacode
     88 is a string (or integer) of varying length. The Array_Address_Id is a string with
     89 a fixed lenght of 10 characters that consists of an Illuminacode padded with zeros.
    8890 - ''' N ''': The total number of beads used to calculate Mean GRN and Dev GRN.
    8991 - ''' Mean GRN ''': The mean intensity.
    … …  
    9597
    9698
    97 == Illumina Sentrix® Array binary manifest (BGX) files ==
    98 
    99 In addition to IDAT files, BeadStudio requires Illumina Sentrix® Array binary
     99== Illumina Sentrix Array binary manifest (BGX) files ==
     100
     101In addition to IDAT files, BeadStudio requires Illumina Sentrix Array binary
    100102manifest (BGX) files that contain information about the probes on a specific
    101 Illumina Sentrix® Array, including gene symbol, probe sequence, and so on.
     103Illumina Sentrix Array, including gene symbol, probe sequence, and so on.
    102104In BASE, the BGX files are used to create array designs that describe the probe
    103 content of a specific Illumina Sentrix® Array.
     105content of a specific Illumina Sentrix Array.
    104106
    105107BGX files are tab separated text files composed of 3 sections named Heading,

  • plugins/base2/net.sf.basedb.illumina/trunk/build.xml

    r970 r1032  
    2222  <property name="javac.source" value="1.5" />
    2323  <property name="javac.target" value="1.5" />
    24   <property name="javac.encoding" value="ISO-8859-1" />
     24  <property name="javac.encoding" value="UTF-8" />
    2525  <property name="depend.jars"
    2626    value="http://base2.thep.lu.se/base/jars/2.9.0"

  • plugins/base2/net.sf.basedb.illumina/trunk/config/illumina-extended-properties.xml

    r624 r1032  
    1 <?xml version="1.0" ?>
     1<?xml version="1.0" encoding="UTF-8" ?>
    22<!DOCTYPE extended-properties SYSTEM "extended-properties.dtd" >
    33<!--

  • plugins/base2/net.sf.basedb.illumina/trunk/config/illumina-raw-data-types.xml

    r572 r1032  
    1 <?xml version="1.0" ?>
     1<?xml version="1.0" encoding="UTF-8" ?>
    22<!DOCTYPE raw-data-types SYSTEM "raw-data-types.dtd" >
    33<!--

  • plugins/base2/net.sf.basedb.illumina/trunk/src/net/sf/basedb/illumina/plugins/DetectionPValue.java

    r941 r1032  
    22  $Id$
    33
    4   Copyright (C) 2008 Jari Hakkinen
     4  Copyright (C) 2008 Jari Häkkinen
    55
    66  This file is part of Illumina plug-in package for BASE.
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