We have developed regression methods for the normalization and estimation of error in expression profiles. The analysis is based on the representation of expression patterns as vectors in intensity space.
Normalization is associated with the identification of a reference line for the expression vectors.
The parameters for the reference line are obtained using a general linear least squares procedure which allows the specification of weights for the intensity data. The weights are chosen in accordance with the expected variation of error with signal intensity. This intensity space analysis is also applied to data for two-color, fluorescence measurements. This is achieved through an additional normalization obtained from the set of control experiments. The variance of the intensity in expression patterns is obtained by the analysis of the deviation of vectors from the reference line, for replicate experiments.