Lumi

Looking for free Illumina software? Lumi is a pipeline to analyze Illumina microarray data at the probe-level, including probe-identifier management (nuID), quarterly updated probe-to-gene mapping and annotation (nuIDblast), probe-intensity transformation (VST) and normalization (RSN), and quality control (QA/QC). By extending the ExprSet object with Illumina-specific features, Lumi is designed to work with other Bioconductor packages, such as Limma and GOstats to detect differential genes and conduct Gene Ontology analysis.

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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.

Download | Features | Documentation | Support

Related links: llumina Microarrays, Bioconductor, Lumi Blog
References: Lin, S. M. et al., (2006), Model-based variance-stabilizing transformation for Illumina microarray data; Pan, D. et al., (2006), Manufacturer- independent identifier for oligomers.

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Download lumi from Bioconductor
You need the following packages to construct a Illumina data analysis pipeline:

Related Packages
The following two packages in Bioconductor are strongly recommended:

Limma
GOstats.

Northwestern University

Robert H. Lurie Comprehensive Cancer Center

The page is located at http://basic.northwestern.edu/projects/lumi Created 11-18-06 Last updated 3-12-07