ArrayPipe Online Documentation

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Introduction

ArrayPipe aims to provide a flexible tool for visualizing and processing of microarray data. It is currently geared towards two-colour slides. Results are generated in web-browsable HTML format.

This tool comprises a set of functions that can be configured and assembled to suit the user's need. To provide maximal automation, ArrayPipe can also be run from the command line. This tutorial only covers the usage through the WWW. It will guide you through the steps of logging on, inserting data, carrying out some processing and working with the results.

Note

ArrayPip tries to give the users maximum flexibility, allowing them to freely configure the processing steps applied to their data. This puts the responsibility on the user to ensure the selected steps and the order in which they are applied make sense and are statistically correct!

Navigation

ArrayPipe results pages are divided into multiple sections. The initial layout of the output page is as follows:
Info section
(guidance and links)
Data Files
(settings for columns and array layout)
Action section
(action menu and start buttons)
Settings section
(parameter tuning)
Input section
(load files and lists)

However, this changes as you progress through the analysis. The 'Info' section will always stay at the top, but below that you will find the most important section for the according processing step. For example, after loading some data files you will find these listed there, but after each analysis an updated results section will appear near the top:
Info section
(guidance and links)
 
Results section
 
Action section
(action menu and start buttons)
Settings section
(parameter tuning)
Data Files
(settings for columns and array layout)
Input section
(load files and lists)

Some of the sections can get fairly large, which would make scrolling quite tedious. Therefore it is best to use the links in the info section to quickly navigate around the page.

Tip: Rather then scrolling to the top simply hit the 'Home' button on your keyboard or use the [INFO] links scattered throughout the page.

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last modified $Date: 2007/08/27 14:02:03 $
for questions or remarks e-mail karsten_hokamp@sfu.ca.