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TWO COLOR DATA MANAGEMENT TOOL

About
Features
Output files
Documentation
System Requirements
 
Launch Latest Release - 1.0 build 1 (RC1)

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About

  The Two Color Data Management Tool provides a front-end to HDBStat! by taking two color microarray data in the standard GenePix (GPR) format and exporting output files compatible with the format required by the HDBStat! software. However, the user is expected to make minor modification to the output files to suit their experimental design. Please see section output files for more information.

Features

  1. Data Import:
    Only GenePix (GPR) format is supported at this time.
    • If you have not modified the column names in data files, select the "Standard GPR headers" option.
    • If you have modified column header in all of your data files and the change is uniform across all chips, select the "Customized column headers, uniform across chips" option.
    • If you have modified column header in few of your data files, select the "Customized column headers, non-uniform across chips" option.

     
  2. Column Matching:
    For each data file, you must provide column names indicating the columns with values for the following:
    • Channel1 foreground intensity
    • Channel2 foreground intensity
    • Channel1 background intensity
    • Channel2 background intensity

     
  3. Data Output:
    Following options of output are provided:
    • One column per chip
      • Channel1/Channel2 intensity ratio
      • Channel2/channel1 intensity ratio
      • Background corrected Channel1/Channel2 intensity ratio
      • Background corrected Channel2/Channel1 intensity ratio
    • Two columns per chip
      • Foreground intensities for each channel
      • background corrected intensities for each channel
    Based on the selection, appropriate columns are selected from each GPR file and output to one Excel CSV format file.

Output Files

File Names Description
Excel CSV formatted file
(Input files for HDBStat! software. Click here for more information on setting up HDBStat! input files.)
master table.csv HDBStat! Gene Expression Data File formatted output. Users are requested to modify this file by dropping the column named Probe ID in order to make this output file compatible to HDBStat!'s Gene expression data file format.
chip level info table.csv HDBStat! Chip Level Info file formatted output. Users are requested to modify this file by adding the class variables information in the second column.
 Plots
MA Plot <chip-name>.png  MA plots show the intensity-dependant ratio of raw microarray data

Documentation

System Requirements

  • Java 2 Runtime Environment (Version 1.4.2 is recommended, we do not yet recommend using 1.5.0)
  • Microsoft Windows, Linux, Solaris, Mac OS (any operating system that supports J2RE)
  • 256 MB minimum RAM required (512 MB or higher recommended)
  • Minimum of 25 MB of available disk space