RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis.
Bioinformatics
; 22(22): 2825-7, 2006 Nov 15.
Article
em En
| MEDLINE
| ID: mdl-16982708
ABSTRACT
UNLABELLED While meta-analysis provides a powerful tool for analyzing microarray experiments by combining data from multiple studies, it presents unique computational challenges. The Bioconductor package RankProd provides a new and intuitive tool for this purpose in detecting differentially expressed genes under two experimental conditions. The package modifies and extends the rank product method proposed by Breitling et al., [(2004) FEBS Lett., 573, 83-92] to integrate multiple microarray studies from different laboratories and/or platforms. It offers several advantages over t-test based methods and accepts pre-processed expression datasets produced from a wide variety of platforms. The significance of the detection is assessed by a non-parametric permutation test, and the associated P-value and false discovery rate (FDR) are included in the output alongside the genes that are detected by user-defined criteria. A visualization plot is provided to view actual expression levels for each gene with estimated significance measurements. AVAILABILITY:
RankProd is available at Bioconductor http//www.bioconductor.org. A web-based interface will soon be available at http//cactus.salk.edu/RankProd
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Base de dados:
MEDLINE
Assunto principal:
Metanálise como Assunto
/
Biologia Computacional
/
Perfilação da Expressão Gênica
Tipo de estudo:
Prognostic_studies
/
Risk_factors_studies
/
Systematic_reviews
Idioma:
En
Ano de publicação:
2006
Tipo de documento:
Article