General Instructions for Use of ArrayPipe

The following steps comprise the basic usage of the ArrayPipe web server:
  1. Data Upload
  2. Data Settings
  3. Action Setup
  4. Start Process
  5. More Help
Please see below or follow the links above to see more information for each section.

Data Upload

To load data into the tool, you can either choose some of the example files (if provided by the ArrayPipe operator) or use some of your own files. These can be compressed (with gzip or WinZip) to reduce the size and the uploading time. To make transferring of multiple files more convenient, you can also combine them into a single (compressed) archive through tar or WinZip.
The initial upload page will be presented after entering or logging on to the site. Only after data loading will you be able to choose some action steps.

Data Settings

ArrayPipe needs to know certain information about the loaded files. These are:
  1. Array layout:
    This is important for proper visualization of the chip, from which the data was derived.
  2. Data columns:
    Specify which columns contain the Spot ID, and the background and intensity values for each channel, as well as the flags.
  3. Channel labelling:
    This is optional and serves to put the according lables to the output (Cy3/Cy5 or Au/Ag).
  4. Channel annotation:
    Functions like t-tests require information about which channel contains the control and which the treatment. This needs to be inserted by the user.


Action Setup

After uploading and setting up the data, you need to configure the action steps that you would like to run the data. You can compile them from scratch in the Action Chain menu or you can load previously saved settings.
For each action step you can find a paragraph in the Settings Section where the parameters for a particular module can be modified.

Start Process

Once you have configured your action steps, locate the 'Do it!' button at the top and bottom of the page or at the end of the Action Chain menu and click on it. The process will begin and you will be presented with intermediate results pages that refresh themselves until the process is finished and the results page is complete.
You can continue from that page with modified data and action setup.

Please note: To be able to return to your results it is necessary to bookmark the page!

More Help

For more help, please refer to the online tutorial. See also the main ArrayPipe page for contact information.


last modified on Thu Apr 15 12:30:41 PDT 2004
for questions or remarks e-mail karsten_hokampREMOVECAPS@sfu.ca.