Choosing the design parameters for protein lysate arrays

Protein lysate array is a new technology for measuring the relative expressions of proteins, where the array image provides information about the concentrations (expressions) of a given protein for tens of patients or tissues. The array consists of replicated and serially diluted versions of the protein concentration for the biological samples at several spots. When producing the lysate array the experimenter has to set several parameters, such as: the concentration of the sample solution to be printed at a certain spot, the number of dilutions, the number of replicates for each biological sample, and the dilution factor. Having the resulting image of intensities at all spots one can assume a nonlinear model and estimate the values of the relative protein expression levels for all biological samples. In this paper we study how the obtained model can be used to improve the design of the experiment, such that if a second lysate array will be produced, better design parameters will be selected. We propose a methodology for choosing the design parameters, and illustrate it with results for several lysate array data sets.