Two-color spotted arrays are scanned on a ScanArray Express HT scanner and the images are analyzed and gridded with ScanArray software Express v3.0. Agilent and Nimblegen manufactured arrays are scanned on an Axon 4000B scanner. Images from Agilent arrays are gridded and analyzed with Genepix Pro v6.1; whereas, Nimblegen images are gridded and analyzed with Nimblescan v2.4. Typically scanner laser power is kept constant for Cy3/Cy5 scans, and photomultiplier tube values are set for optimal intensity with minimal background. An additional scan is often done for each slide with the PMT set such that <1% of the elements are saturated in order to characterize spots which are saturated at the higher PMT setting.

Illumina beadarrays are scanned on the Illumina® Beadstation 500 to detect Cy3 and Cy5 fluorescence at 532 nm and 633 nm, respectively, with a resolution of 0.8 µm. The images are decoded with Illumina Beadscan software and analyzed with Illumina Beadstudio.

All data (images and raw numeric data) are made available to the customer via FTP download, which can be accomplished with any computer with a high-speed connection to the internet.