On Microarray Analysis, Objects, Patterns and Bioconductor:

Abstract

Bioconductor was released in May 2002. It has thus been in circulation for a little over a year. The development began in 2000-2001. R-based analysis permits more sophistication than proprietary 'black-box ' tools. Although standard R is very useful, there are significant barriers to entry for nonstatisticians doing microarray analysis in pure R. Bioconductor has removed some of those barriers. It has achieved success within the community and is a nascent standard. However, developing to the Bioconductor standard is not trivial. Moreover, many biologists throw up their hands at learning the sometimes cryptic software combined with inexperience at overcoming the mathematical and computational barriers. As we see it, any well developed microarray analysis framework has three ideal roles which give tension to the design process: It should: 1) provide fairly easy entry points to computationally unsophisticated users. 2) provide an easily extensible framework for continuous analysis development in multiple microarray platforms.