Sam BaushkeM.S. 2005-2007 CV |
Analysis of DNA Microarray Data for Parallel Microbial Detection and Mixed Community FingerprintingComplexities specific to analysis of microarray-based methods for parallel microbial detection include identification of non-specific hybridization and data handling. Non-equilibrium dissociation curves have the potential to identify non-specific hybridizations on these high throughput, diagnostic microarrays, but have traditionally relied on comparison of perfect match and mismatch dissociations. This dependency requires extra experiments or expensive preparation steps. We have developed a method that uses a combination of empirical modeling and theoretical prediction, which successfully screens out most non-specific hybridizations and allows a simplified approach to high throughput analysis. As this analysis is computationally intensive, we have also developed tools using Microsoft Visual Basic (VBA) and Microsoft Excel for the automatic extraction and processing of data from an experiment. The tools automate the processes of extracting the data from text files, replicate averaging, and non-linear curve fitting and then apply the method described above to give the most reliable answer to the question, “What was in my sample?”
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