BayBoots: a model-free Bayesian tool to identify class markers from gene expression data
Genet. mol. res. (Online)
; 5(1): 138-142, Mar. 31, 2006. graf
Article
em En
| LILACS
| ID: lil-449138
Biblioteca responsável:
BR1.1
ABSTRACT
One of the goals of gene expression experiments is the identification of differentially expressed genes among populations that could be used as markers. For this purpose, we implemented a model-free Bayesian approach in a user-friendly and freely available web-based tool called BayBoots. In spite of a common misunderstanding that Bayesian and model-free approaches are incompatible, we merged them in the BayBoots implementation using the Kernel density estimator and Rubin 's Bayesian Bootstrap. We used the Bayes error rate (BER) instead of the usual P values as an alternative statistical index to rank a class marker's discriminative potential, since it can be visualized by a simple graphical representation and has an intuitive interpretation. Subsequently, Bayesian Bootstrap was used to assess BER 's credibility. We tested BayBoots on microarray data to look for markers for Trypanosoma cruzi strains isolated from cardiac and asymptomatic patients. We found that the three most frequently used methods in microarray analysis:
t-test, non-parametric Wilcoxon test and correlation methods, yielded several markers that were discarded by a time-consuming visual check. On the other hand, the BayBoots graphical output and ranking was able to automatically identify markers for which classification performance was consistent. BayBoots is available at http//www.vision.ime.usp.br/~rvencio/BayBoots.Palavras-chave
Texto completo:
1
Coleções:
01-internacional
Base de dados:
LILACS
Assunto principal:
Trypanosoma cruzi
/
Teorema de Bayes
/
Genes de Protozoários
/
Análise de Sequência com Séries de Oligonucleotídeos
/
Modelos Genéticos
Tipo de estudo:
Prognostic_studies
Limite:
Animals
/
Humans
Idioma:
En
Revista:
Genet. mol. res. (Online)
Assunto da revista:
BIOLOGIA MOLECULAR
/
GENETICA
Ano de publicação:
2006
Tipo de documento:
Article
País de afiliação:
Brasil