In summary, commercially available human genomic microarrays from five manufacturers were used to compare Human Brain Total RNA against Universal Human Reference RNA prepared at two different starting amounts. Data comparability was assessed both within and between replicate arrays from the same manufacturer, and across platforms through a comparison of genes common to all systems. Using the spotted arrays, (four out of the five manufacturers) three different image-processing packages were evaluated, and data comparability from six normalisation strategies was also assessed. Results from genes common across all arrays were compared to equivalent assays prepared on other platforms such as Real-Time Reverse Transcriptase quantitative Polymerase Chain Reaction (RT-qPCR).