lumi:: a pipeline for processing Illumina microarray
lumi:: a pipeline for processing Illumina microarray
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DOI：
10.1093/bioinformatics/btn224
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发表时间：
2008-07-01
期刊：
影响因子：
5.8
通讯作者：
Lin, Simon M.
中科院分区：
文献类型：
--
作者：
Du, Pan;Kibbe, Warren A.;Lin, Simon M.
Illumina微阵列正在成为流行的微阵列平台。Illumina的BeadArray技术使其预处理和质量控制不同于其他微阵列技术。不幸的是，大多数其他分析都没有利用BeadArray系统的独特特性，只是采用了最初为AffyArray微阵列设计的预处理方法。lumi是一个专为处理Illumina微阵列数据而设计的Bioconductor软件包。它包括数据输入、质量控制、方差稳定、标准化和基因注释等部分。具体而言，lumi软件包包括方差稳定转换（VST）算法，该算法利用了每个Illumina微阵列上可用的技术重复。软件包中提供了不同的标准化方法选项和多个质量控制图。为了更好地注释Illumina数据，设计了独立于供应商的核苷酸通用标识符（nuID）来识别Illumina微阵列的探针。nuID注释包和lumi处理结果的输出可以轻松地与其他Bioconductor包集成，以构建Illumina数据的统计数据分析管道。
Illumina microarray is becoming a popular microarray platform. The BeadArray technology from Illumina makes its preprocessing and quality control different from other microarray technologies. Unfortunately, most other analyses have not taken advantage of the unique properties of the BeadArray system, and have just incorporated preprocessing methods originally designed for Affymetrix microarrays. lumi is a Bioconductor package especially designed to process the Illumina microarray data. It includes data input, quality control, variance stabilization, normalization and gene annotation portions. In specific, the lumi package includes a variance-stabilizing transformation (VST) algorithm that takes advantage of the technical replicates available on every Illumina microarray. Different normalization method options and multiple quality control plots are provided in the package. To better annotate the Illumina data, a vendor independent nucleotide universal identifier (nuID) was devised to identify the probes of Illumina microarray. The nuID annotation packages and output of lumi processed results can be easily integrated with other Bioconductor packages to construct a statistical data analysis pipeline for Illumina data.