A framework for oligonucleotide microarray preprocessing

被引：1124

作者：

Carvalho, Benilton S. ^{[1
]}

Irizarry, Rafael A. ^{[2
]}

机构：

[1] Univ Cambridge, Dept Oncol, CRUK Cambridge Res Inst, Li Ka Shing Ctr, Cambridge CB2 0RE, England

[2] Johns Hopkins Univ, Dept Biostat, Bloomberg Sch Publ Hlth, Baltimore, MD 21205 USA

来源：

BIOINFORMATICS | 2010年 / 26卷 / 19期

基金：

美国国家卫生研究院;

关键词：

GENOTYPE CALLS; PROBE LEVEL; ARRAY DATA; NORMALIZATION; EXPLORATION; SOFTWARE;

D O I：

10.1093/bioinformatics/btq431

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Motivation: The availability of flexible open source software for the analysis of gene expression raw level data has greatly facilitated the development of widely used preprocessing methods for these technologies. However, the expansion of microarray applications has exposed the limitation of existing tools. Results: We developed the oligo package to provide a more general solution that supports a wide range of applications. The package is based on the BioConductor principles of transparency, reproducibility and efficiency of development. It extends the existing tools and leverages existing code for visualization, accessing data and widely used preprocessing routines. The oligo package implements a unified paradigm for preprocessing data and interfaces with other BioConductor tools for downstream analysis. Our infrastructure is general and can be used by other BioConductor packages.

引用

页码：2363 / 2367

页数：5

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