From Array Suite Wiki
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.
After installing R and RStudio, use the following command within RStudio to install lumi and dependencies.
source("https://bioconductor.org/biocLite.R") biocLite("lumi") library(lumi)
Go to ArrayStudio -> Tools -> R Integration -> Set R Script Engine, check the box in front of lumi, click Update button, the package and script will be updated automatically.