  The lack of specificity in microarray experiments due to non-specific
hybridization raises a serious problem for the analysis of microarray data
because the residual chemical background intensity is not related to the
expression degree of the gene of interest. We analyzed the concentration
dependence of the signal intensity of perfect match (PM) and mismatch (MM)
probes in terms using a microscopic binding model using a combination of mean
hybridization isotherms and single base related affinity terms. The signal
intensities of the PM and MM probes and their difference are assessed with
regard to their sensitivity, specificity and resolution for gene expression
measures. The presented theory implies the refinement of existing algorithms of
probe level analysis to correct microarray data for non-specific background
intensities.
