Coupled thermal-electric computational mechanics techniques have been developed to understand the temperature distribution along a special design spring and cantilever probe body in order to model the probe burn phenomenon for conduction.
In addition, it uses τ i to model the probe specific variability expected in a single experimental condition.
Another popular method, represented by MAT (Johnson et al., 2006), uses probe sequences to model the probe effects.
As in Carvalho et al. (2007), we model the probe sequence affinity as a function of nucleotide and position in order to control for (i) small fluctuations in probe affinities across arrays, and (ii) differences in PMA and PMB affinities.
For older chip types (10 500K) for which the replicated probes are slightly shifted along the genome, it is still sensible to model the probe affinities using a multi-array model such as the log-additive model used in CRMA v1.
In the Langmuir model, the probe intensity is given as follows: (1) where α gives the scale of intensity, K gives the equilibrium constant of probe target duplex formation, x gives the concentration of target molecules and I bg denotes the optical background intensity.
