Several two-step methods can be used to analyze cDNA microarray gene expression data containing biological and technical replications. In this study, an ANOVA normalization-based method (M1) and a LOWESS normalization-based method (M2) were compared and a compromise implementation (M3) was proposed. The results from analysis of ovarian growth in prepuberal pigs at different age classes showed large discrepancies between the lists of differentially expressed genes identified by M1 and M2. The proposed method (M3) had similar results to M2. A real data-based simulation demonstrated that M2 was superior to M1 in sensitivity for identifying differentially expressed genes, and M3 further improved the sensitivity by 5.5% over M2 when the simulated inter-class difference was relatively small.
Proceedings of the World Congress on Genetics Applied to Livestock Production, Volume , , 23.03, 2006
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