Functional genomic studies investigate the simultaneous expression of multiple genes under different conditions or instances. In general, the microarray technology is based on the simultaneous hybridization of two labeled (e.g. dyes Cy3 and Cy5) cDNA samples to an array of target sequences. The microarray background intensity is subtracted from the sample intensity and follow-up normalization minimizes the impact of one channel (dye) being systematically brighter than the other. When samples from multiple instances and reference (in every array) are analyzed, the response is the difference between the logarithms of the sample to reference ratio between instances. The identification of expression patterns can be hindered by unaccounted noise including within array variation (e.g. variation in the rate of dye incorporation and spot size) and among array variation originating during the fabrication, hybridization and scanning phases. The large amount of information available poses computational, statistical and interpretational challenges partially addressed by clustering, network, projection and t-test methods. The previous response and approaches have limitations including restricted use of the information contained by the data, limited ability to account for all sources of variation and challenging interpretation of the results.

S. L Rodriguez-Zas, B. R Southey

Proceedings of the World Congress on Genetics Applied to Livestock Production, Volume 2002. Session 16, , 16.04, 2002
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