ImportIlluminaReportLumi.pdf

Overview

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.

Update lumi

Please note that R version 3.6 is strongly recommended for best compatibility

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.