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Bioinformatics Advance Access originally published online on September 27, 2005
Bioinformatics 2005 21(21):4069-4070; doi:10.1093/bioinformatics/bti663
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oxfordjournals.org

A friendly statistics package for microarray analysis

P. Sykacek 1,2,*, R. A. Furlong 2 and G. Micklem 1,3

1Department of Genetics, University of Cambridge UK
2Department of Pathology, University of Cambridge UK
3Cambridge Computational Biology Institute at the Department of Applied Mathematics and Theoretical Physics, University of Cambridge UK

*To whom correspondence should be addressed.

Summary: The friendly statistics package for microarray analysis (FSPMA) is a tool that aims to fill the gap between simple to use and powerful analysis. FSPMA is a platform-independent R-package that allows efficient exploration of microarray data without the need for computer programming. Analysis is based on a mixed model ANOVA library (YASMA) that was extended to allow more flexible comparisons and other useful operations like k nearest neighbour imputing and spike-based normalization. Processing is controlled by a definition file that specifies all the steps necessary to derive analysis results from quantified microarray data. In addition to providing analysis without programming, the definition file also serves as exact documentation of all the analysis steps.

Availability: The library is available under GPL 2 license and, together with additional information, provided at http://www.ccbi.cam.ac.uk/software/psyk/software.html#fspma

Contact: peter{at}sykacek.net

Received on February 21, 2005; revised on July 18, 2005; accepted on September 5, 2005

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