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Comparability of gene expression measurements on microarrays
DNA microarray platforms and applications are undergoing rapid development, but creating reproducible data with a high level of consistency across experiments and various platforms is widely accepted by the scientific community as a major problem. This project aimed to address some of these concerns by experimentally evaluating the comparability of gene expression measurements on microarrays performed on different microarray systems. An evaluation of a selection of normalisation strategies currently in use for array-based experiments was also addressed. An assessment of the effect of using different software packages for image processing and downstream analysis on data comparability is another major output of the project.
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).
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