Abstract: A modified principal component analysis technique is described herein for analysis of relatively small data sets for the detection of chromosomal aneuploidies and/or microdeletions. Unlike analysis techniques for microarray studies, the present technique uses a modified principal component analysis that does not involve performing a covariance analysis. The methods, systems, and apparatus described herein allow for significant reduction of data noise in tests for the detection of chromosomal aneuploidies and/or microdeletions, leading to fewer inconclusive results.