OOMAL is being replaced by a set of R libraries using S4 classes and compatible with BioConductor. See OOMPA for the latest release.

Object Oriented Microarray Library in S-PLUS

Version 4.0

The Object Oriented Microarray Library in S-PLUS is a suite of object-oriented programming modules written in S-PLUS for the analysis of microarray experiments. The library contains tools for analyzing both experiments conducted with two-color fluorescence-labeled targets on glass slides as well as experiments conducted with radioactive isotope-labeled targets on nylon membranes. In the present version, tools are available for analyzing single-slide fluorescence experiments and arbitrary isotope experiments where the primary scientific question is to determine the genes that are statistically significantly differentially expressed betwen two groups. We expect to enhance the capabilities of the library in the future.

The entire library can be compiled by running the script microarrays.ssc, which sources the remaining sections of code, including all the built-in designs.

As part of the library, we have made it a point to include tools that make it easy to generate a standard set of reports that can be delivered by the bioinformatician to the biologist.

The library also defines a number of general utility functions.

Classes Defined in the Library

Basic Analysis of Replicated Radiolabeled Experiments

Additional Classes for Two-Color Fluorescence Using Within-Slide Replication

Additional Tools

Generic Methods

The library defines several new generic methods.

analyze(object, ...)
In general, this method represents an expensive computational step carried out in preparation for a graphical display, but the semantics may differ from class to class. The default implementation of the method performs the null analysis; that is, the return value is identical to the object that is passed in as the first argument.
extract(object, ...)
This is a generic method to extract columns of particular measurements from structures containing many such columns. See the description of the channel package for a discussion of standard extractor routines.
transform(object, ...)
This is a generic method to transform columns of particular measurements. See the description of the channel package for a discussion of standard transformer routines.