Merlin: Microarray Analysis Pipeliner and Parallelization

	Merlin Microarray Analysis Engine and BioConductor Parallelization	Development funded by Genome Canada &
	Sun Center of Excellence for Visual Genomics University of Calgary, Canada

Merlin consists of Java code that creates, runs and reformats R/BioConductor analysis. Merlin focuses on enabling analysis of several hundred chips at once, in a high throughput manner. Merlin was originally developed, and is currently being used as, the microarray analysis engine for the Transplant Transcriptome Project at the University of Alberta.

The prerequisites for using Merlin are:

R version 2.10
BioConductor version 2.5
Java 1.5 or better
A Java Servlet container, such as Tomcat (if you want to use the Web interface) Tomcat Quick Install Guide

If you have all of the prerequisites, you can download the Merlin Java archive for command line use, or download the Merlin Web archive for Web-based use. Documentation on running Merlin can be found here.

R/Bioconductor Packages

The following packages have been partially parallelized for systems supporting POSIX threads, and are now part of the Bioconductor distribution (thanks to Ben Bolstad):

affy: microarray analysis methods (requires that the FFTW library be installed on your computer for full parallelization)
affyio: microarray data loading
preprocessCore: utilities for data normalization, etc.

To enable multithreading, define the command-shell environment variable R_THREADS before starting R, setting it to the number of concurrent threads you'd like to run.

GeneSpring plug-in

This plug-in allows you to import Merlin results spreadsheets into GeneSpring. The zip file contains a PDF file of installation instructions, but essentially, simply dragging the zip file over an open GeneSpring window will cause the plug-in to be installed.

For developers

The annotated DTD for specifying an analysis request can be found in the Merlin JAR file, and here. The Java source code of Merlin is available under the GNU Public License.

Using new algorithms

Please see this page to find out how to add your favorite array algorithm to Merlin.