lumi **

Lumi is an ongoing project for Illumina microarray data analysis, including the design of a software package in R/Bioconductor and the discussion of microarray experiment design.

** an open source project at the Bioinformatics Core of the Robert H. Lurie Comprehensive Cancer Center, Northwestern University.


Lumi Package: Architecture

lumiR: data I/O. read in Illumina data file.
lumiQ: quality control
lumiT: variance-stabilizing data transformation
lumiN: normalization
lumi: all-in-one Illumina data processing, including all the aboves.

There will be a data package and an annotation package. I have discussed the annotation package with Lynn Amon at University of Washington.

The down-stream analysis will follow the existing infrastructure in the Bioconductor package, since we use the exprSet (eSet).


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