dChip: Automated analysis

Automating dChip functions

See details in Li 2008, BMC Bioinformatics. [V12/12/07+] Use “Tools/Automate”.

Demonstration data package: Download this file (90 MB), unzip files into a directory and click dchip.exe to run several automated menu functions.

Older method

[V8/11/07+; Forum thread] In the Windows "Command Prompt" window ("Start menu/Run/cmd"), one can go to the dchip.exe directory and type command such as "dchip2006 -ini lung_10k.ini -norm -model -export -log" to automate some dChip data processing functions. First, make a parameter setting file (with ".ini" suffix) by these example steps:

1. Manually run dChip to open a group of CEL files with a group name (e.g. lung_10k). Specify parameters in "Open Group/Options" and "Normalize & Model/Options" as usual and click "OK". Once the analysis starts, use ESC key to stop the analysis.

2. lung_10k.ini file will be generated in the same directory as dchip.exe. It contains most dChip parameters specified through dialogs.

3. lung_10k.ini can also be modified in text editor as to CDF file names, data directories, etc.

Next, in the "Command Prompt" window, type dChip executable file name "dchip2006" followed by one or more options below (dashes '-' indicate options and spaces separate them):

-ini my_group_name.ini: reading in existing group settings and perform "Analysis/Open group"

-norm, -model: perform "Analysis/Normalization & Model"

-export: perform "Tools/Export expression value" to export data of all samples and probe sets

-log: perform "Analysis/Save Log" to save a log file after all analysis are finished

(page created 12/12/07)