Abstract
A new method for aligning families of two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) images arising in proteomics studies is presented. Forward piecewise bilinear transformations are used to determine an ideal gel and to obtain an initial alignment of the family of gels to this ideal gel. Both the ideal landmarks and the coefficients defining the transformations are obtained by solving a quadratic programming problem. The alignment is then improved by using inverse transformations on finer grids. Numerical results for a family of 123 gels are reported.
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