SpotWhatR: a user-friendly microarray data analysis system
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Data
2006
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Resumo
SpotWhatR is a user-friendly microarray data analysis
tool that runs under a widely and freely available R statistical language
(http://www.r-project.org) for Windows and Linux operational systems.
The aim of SpotWhatR is to help the researcher to analyze microarray
data by providing basic tools for data visualization, normalization, determination
of differentially expressed genes, summarization by Gene Ontology
terms, and clustering analysis. SpotWhatR allows researchers
who are not familiar with computational programming to choose the most
suitable analysis for their microarray dataset. Along with well-known
procedures used in microarray data analysis, we have introduced a standalone
implementation of the HTself method, especially designed to find
differentially expressed genes in low-replication contexts. This approach
is more compatible with our local reality than the usual statistical meth-ods. We provide several examples derived from the Blastocladiella
emersonii and Xylella fastidiosa Microarray Projects. SpotWhatR is
freely available at http://blasto.iq.usp.br/~tkoide/SpotWhatR, in English
and Portuguese versions. In addition, the user can choose between “single
experiment” and “batch processing” versions.
Descrição
Palavras-chave
Microarray data analysis, Gene ontology, Data vizualization, User-friendly system, Clustering, Normalization
Citação
KOIDE, Tie et al. SpotWhatR: an user-friendly microarray data analysis system. Genetics and Molecular Research, Ribeirão Preto, v. 5, n. 1, p. 93-107, 2006.