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Lumi, an open-source package written in R to analyze Illumina microarray data at the probe-level. Designed to work with Limma, GOstats and others packages in the Bioconductor.

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Recommended Illumina workflow

transformation  

VST transformation
Logarithm is a special case of Variance-Stabilizing Transformation (VST).

normalization  

RSN normalization
Robust Spline Normalization (RSN) combines features of quantile and loess. 

QA/QC  

QA/QC
Various plots and outlier detection methods.

limma  

Limma
Find differentially expressed genes by empirical Bayes correction of linear models; a bioconductor package by G. K. Symth.

GOstats  

GOStats
Conduct Gene Ontology (GO) analysis of a gene list; a bioconductor package by R. Gentleman.