Cocas - ChIP On Chip Analysis Suite Online Help

1. Introduction
2. Requirements
3. Getting started
4. Using CoCAS

1. Guided Wizard
2. Loading files
3. Dye swap
4. Intra-array normalization parameters
5. Inter-array normalization parameters
6. Replicate merge method
7. P-value estimation
8. Output format
9. Peak detection
10. QC Reports
11. Output

    5.   Changes from previous versions

    1.   Introduction

CoCAS is a standalone Chromatin immunoprecipitation microarray (ChIP-on-chip) analysis application. It has been designed to be used primarily on Agilent microarrays, be they scanned using an Agilent scanner or with a GenePix scanner. CoCAS is free software and builds upon existing packages in Java and R programming languages, notably BioConductor. CoCAS uses Java for user graphical interface, and R for the bulk of the calculations.

    2.   Requirements

CoCAS requires at least 1 Gb RAM and a 2GHz Intel Pentium 4 or equivalent for comfortable use. We recommend at least 1 Gb of free hard disk space for swapping. CoCAS runs under any 32-bit or 64-bit version of Microsoft Windows. NOTE THAT CoCAS REQUIRES R VERSION 2.5.x/2.6.x TO BE INSTALLED ON YOUR SYSTEM (THERE ARE COMPATIBILITY ISSUES WITH R 2.7.x, WE ARE CURRENTLY WORKING ON THEM) AS WELL AS JAVA 1.5. JAVA 1.6 IS RECOMMENDED.

    3.  Getting started

CoCAS can be readily started by double clicking on the CoCAS_2.4.jar icon. Alternatively, CoCAS may be run from the command line with specific parameters, for example, in order to assign more memory to CoCAS, one would type java -Xmx2048m -jar [path to CoCAS]/CoCAS_2.4.jar . A welcome screen will prompt you to use the express wizard, which is an easy step by step guide.

Upon first use, you should click "No" so that you can check that you have all the required libraries. You can do this by clicking on the "Libraries" menu item from the "Update" menu.

CoCAS will then check and download libraries where appropriate. This process can be quite lengthy.

 

    4.  Using CoCAS

1. Guided Wizard

CoCAS features a simple wizard that can help you design your analysis. There are eight steps which provide detailed help. The first step is to define an analysis name. Then comes file loading which is explained in the next section.

 

2.  Loading Files

Files can be loaded three ways in CoCAS. One way is to use the step-by-step guided wizard, or from the main window, either by right clicking on the File Panel, or by using the File Menu. In the classic mode, once you have loaded files, the main panel, which was greyed out, becomes accessible. CoCAS allows you to enter all replicas of a same experiment under one slide. For example, if you have two replicas of one experiment, 252040810001 and 252040810002, you will enter them under slide 1 for example