How does GPAP account for technical replicates on a single slide?
If you have replicates evenly printed on your slide such that replicate features have an equal number of rows between each replicate in the GPR files and are separated by an equal number of features on the array, GPAP can average these replicates (after filtering and normalization) and provide averaged results and overall B-statistics for each gene. This works when the replicates are printed in different replicate arrays. Suppose your microarray was printed using 16 pins (4×4 pins) and each sub-array or block contains 18×18 spots (324 features per block) and you have printed duplicate spots in replicate arrays, the replicates would be equally spaced with 16x18x18 = 5184 spots between each replicate and 5184 rows would exist between reach replicate in the GPR files.
