Document Type


Date of Award

Summer 8-31-2002

Degree Name

Master of Science in Computational Biology - (M.S.)


Federated Department of Biological Sciences

First Advisor

Michael Recce

Second Advisor

Ronald Philip Hart

Third Advisor

Peter P. Tolias


Microarray technology is currently one of the most valuable gene expression tools in molecular biology allowing the experimenter to simultaneously quantify the expression of thousands of genes. It is also one of the most difficult tools to use accurately as each microarray produces a large amount of information that needs to be inspected and normalized before analysis. As the size of a microarray or number of replicates increase, the use of manual inspection becomes impractical. The aim of this thesis is to introduce an algorithm that evaluates each feature of a microarray from the scanned data file. A quality score is calculated from various spot parameters, the quality-quotient, and can be used to automatically assess the quality of the spot. This quality-quotient can then be utilized to automatically select quality spots or act as a weighting factor for comparing spots from replicate microarrays.