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Education BeadArray Expression Analysis Using Bioconductor 1,2 3 3,4 1,5 3,4 Matthew E. Ritchie *, Mark J. Dunning *, Mike L. Smith , Wei Shi , Andy G. Lynch 1 Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia, 2 Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia, 3 Cancer Research UK, Cambridge Research Institute, Cambridge, United Kingdom, 4 Department of Oncology, University of Cambridge, Cambridge, United Kingdom, 5 Department of Computer Science and Software Engineering, The University of Melbourne, Parkville, Victoria, Australia The hierarchy of data, from individual points: raw data including the scanned Abstract: Illumina whole-genome pixels that make up beads on a BeadArray TIFF images, bead-level data without the expression BeadArrays are a popu- for a WG-6 BeadChip, is illustrated in TIFF images, summarized output from lar choice in gene profiling studies. Figure 1A. BeadStudio/GenomeStudio, or data ob- Aside from the vendor-provided The experimental process for measur- tained from a public repository. Depend- software tools for analyzing Bea- ing transcript levels in a sample of ing on the format available, different dArray expression data (GenomeS- tudio/BeadStudio), there exists a interest involves labelling RNA