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Bioinformatics Advance Access published online on October 25, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti729
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received May 25, 2005
Revised October 17, 2005
Accepted October 17, 2005

Applications note

ISER: selection of differentially expressed genes from DNA array data by nonlinear data transformations and local fitting

R. D. Drummond 1, A. Pinheiro 2, C. S. Rocha 3, and M. Menossi 1*

1 Laboratório de Genoma Funcional - Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas 13083-875, PO Box 6010, Brazil; Departmento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas, Campinas 13084-971, Brazil
2 Departmento de Estatística, Instituto de Matemática, Estatística e Computação Científica, Universidade Estadual de Campinas, Campinas 13083-859, Brazil
3 Laboratório de Genoma Funcional - Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas 13083-875, PO Box 6010, Brazil

* To whom correspondence should be addressed.
M. Menossi, E-mail: menossi{at}unicamp.br


  Abstract

Summary: This report describes an algorithm (Intensity-dependent Selection of Expression Ratios or ISER) developed to analyse DNA array data by optimising the selection of genes with the most significant variations in expression amongst two RNA samples. The algorithm is designed for use when little or no replication of array hybridizations is available.

Availability: ISER is written in R language, and its code and on-line version are freely available at https://ipe.cbmeg.unicamp.br/pub/PMmA.

Supplementary Material: https://ipe.cbmeg.unicamp.br/pub/ISER.


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