BeadArray Specific Methods for Illumina Methylation and
Expression Microarrays
affy (>= 1.23.4), methylumi (>= 2.3.2), GenomicFeatures,
GenomicRanges, annotate, Biobase (>= 2.5.5), lattice, mgcv (>=
1.4-0), nleqslv, KernSmooth, preprocessCore, RSQLite, DBI,
AnnotationDbi, MASS, graphics, stats, stats4, methods
beadarray, limma, vsn, lumiBarnes, lumiHumanAll.db,
lumiHumanIDMapping, genefilter, RColorBrewer
Pan Du, Richard Bourgon, Gang Feng, Simon Lin
The lumi package provides an integrated solution for the Illumina microarray data analysis. It includes functions of Illumina BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific variance stabilization, normalization and gene annotation at the probe level. It also includes the functions of processing Illumina methylation microarrays, especially Illumina Infinium methylation microarrays.
Microarray, OneChannel, Preprocessing, DNAMethylation,
QualityControl, TwoChannel