Changeset 1032 for plugins/base2/net.sf.basedb.illumina/trunk/README

Timestamp:

Apr 7, 2009, 8:24:34 AM (14 years ago)

Author:

Nicklas Nordborg

Message:

Fixes #202: Change source files to UTF-8

File:

• plugins/base2/net.sf.basedb.illumina/trunk/README (modified) (7 diffs)

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

@@ -29 +29 @@
  
  2. Illumina Bead Summary (IBS) files. The IBS files contain quantified probe intensities.
- 3. Illumina Sentrix® Array binary manifest (BGX) file. The BGX files contain probe annotations.
+ 3. Illumina Sentrix Array binary manifest (BGX) file. The BGX files contain probe annotations.
  
 For SNP experiments:
@@ -46 +46 @@
 
 The Illumina BeadArray Reader is a scanner that can read arrays including Illumina 
-Sentrix® BeadChips and Sentrix® Array Matrices (SAMs). Operation of the BeadArray 
-Reader and image aquisition from Sentrix® arrays is handled by the Illumina BeadScan 
+Sentrix BeadChips and Sentrix Array Matrices (SAMs). Operation of the BeadArray 
+Reader and image aquisition from Sentrix arrays is handled by the Illumina BeadScan 
 software.
 
@@ -54 +54 @@
 as the Illumina BeadStudio software. 
 
-The Illumina plug-ins package for BASE reads Illumina Sentrix® Array data from 
+The Illumina plug-ins package for BASE reads Illumina Sentrix Array data from 
 Illumina Bead Summary (IBS) files. The IBS files are not by default outputted by 
 the BeadArray Reader and the scanner must be configured to do so. Once the 
@@ -61 +61 @@
 to contact their local Illumina Field Application Scientist.
 
-The IBS files are text files that contain bead-type level data for scanned Sentrix® 
+The IBS files are text files that contain bead-type level data for scanned Sentrix 
 arrays. The file format is explained in detail in the section Illumina Bead Summary 
 files.
@@ -67 +67 @@
 == Illumina Bead Summary (IBS) files ==
 
-The IBS files contain bead-type level data for scanned Sentrix® arrays. 
+The IBS files contain bead-type level data for scanned Sentrix arrays. 
 The IBS files are simple comma separated text files with file extension .csv. 
 The IBS files are outputted by the BeadArray Reader in the same directory as any 
@@ -85 +85 @@
 The column content in an IBS file is described below.
  - ''' Illumicode ''': A code corresponding to the Array_Address_Id in the 
- 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.
+ 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.
  - ''' N ''': The total number of beads used to calculate Mean GRN and Dev GRN.
  - ''' Mean GRN ''': The mean intensity.
@@ -95 +97 @@
 
 
-== Illumina Sentrix® Array binary manifest (BGX) files ==
-
-In addition to IDAT files, BeadStudio requires Illumina Sentrix® Array binary 
+== Illumina Sentrix Array binary manifest (BGX) files ==
+
+In addition to IDAT files, BeadStudio requires Illumina Sentrix Array binary 
 manifest (BGX) files that contain information about the probes on a specific 
-Illumina Sentrix® Array, including gene symbol, probe sequence, and so on. 
+Illumina Sentrix Array, including gene symbol, probe sequence, and so on. 
 In BASE, the BGX files are used to create array designs that describe the probe 
-content of a specific Illumina Sentrix® Array.
+content of a specific Illumina Sentrix Array.
 
 BGX files are tab separated text files composed of 3 sections named Heading,