Microarray data analysis has been the subject of extensive and ongoing pipeline development due to its complexity, the availability of several options at each analysis step, and the development of new analysis demands, including integration with new data sources. We are available for consultation during the development phase of the analysis and typically help the investigator(s) determine the type of analysis to use, the number of samples and the type of microarray to use.
For expression arrays we provide a report that includes differential expression analysis and we are available to do follow-on analyses (e.g. enrichment testing).
For methylation microarray analysis we use a group of R packages from BioConductor to normalize the signals from each sample for intensity and color bias, correct for differences in background and assess differential methylation.