A colleague needed some help getting Illumina BeadArray gene expression data loaded into R for data analysis with limma. Hopefully whoever ran your arrays can export the data as text files formatted as described in the code below. If so, you can import those text files directly using the beadarray package. This way you avoid getting bogged down with GenomeStudio, which requires a license (ugh) and only runs on Windows (ughhh). Here’s how I do it.