Lumi Package: Architecture
lumiR: data I/O. read in Illumina data file.
lumiQ: quality control
lumiT: variance-stabilizing data transformation
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).