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Bioinformatics Vol. 19 no. 18 2003
pages 2461-2464
© 2003 Oxford University Press

Using credibility intervals instead of hypothesis tests in SAGE analysis

Ricardo Z.N. Vêncio 1,*, Helena Brentani 2,3 and Carlos A.B. Pereira 1

1 Departamento de Estatística, Instituto de Matemática e Estatística da Universidade de São Paulo, São Paulo 04601-003, Brazil, 2 Fundação Antônio Prudente, São Paulo 01509-900, Brazil and 3 Ludwig Institute for Cancer Research, São Paulo 01509-010, Brazil

Received on March 26, 2003 ; revised on June 17, 2003 ; accepted on July 17, 2003

Motivation: Statistical methods usually used to perform Serial Analysis of Gene Expression (SAGE) analysis are based on hypothesis testing. They answer the biologist's question: ‘what are the genes with differential expression greater than r with P-value smaller than P?’. Another useful and not yet explored question is: ‘what is the uncertainty in differential expression ratio of a gene?’.

Results: We have used Bayesian model for SAGE differential gene expression ratios as a more informative alternative to hypothesis tests since it provides credibility intervals.

Availability: The model is implemented in R statistical language script and is available under GNU/GLP copyleft at supplemental web site.

Supplementary information: http://www.ime.usp.br/~rvencio/SAGEci/

Contact: rvencio{at}ime.usp.br

* To whom correspondence should be addressed.


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