Alternative CDF's were generated by masking probes which showed non-specific hybridization towards mouse in the human arrays and vice versa. Briefly, using raw intensity signals from cel files, individual probes were filtered if they met the following criteria: the net intensity (PM-MM) of each probe pair from the cross-reactive species was less than 10 and greater than 50% of the corresponding signal from human tumor core. Alternatively, to detect cross-reactive human signal on the mouse microarrays, mouse chips were hybridized with pure human cell line RNA and the corresponding same criteria were applied. The remaining probes were grouped into their original probe sets and those that had at least 4 remaining probes were retained in the new chip definition file (cdf). This resulted in alternative cdf’s containing 26,954 probe sets for the HG-U133 plus2 array and 21,675 probe sets for the Mouse430_2 array.
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