Comparison Analysis (Experimental vs Baseline arrays)

# Compare the difference values (PM-MM) of each probe pair in the baseline array to its matching probe pair on the experimental array.

# Before comparing two arrays, variations between the two experiments caused by technical and biological factors must be corrected by scaling, normalization or a Robust normalization.

# Change p-value
Using the difference between PM and MM as well as PM and background intensities, the Change p-value is calculated by the Wilcoxon's signed rank test.

# Change Call
Increase (I): p-value < gamma1
Marginal Increase (MI): gamma1 < p-value < gamma2
No Change (NC): gamm2 < p-value < 1-gamma2
Marginal Decrease (MD): 1-gamma2 < p-value < 1-gamma1
Decrease (D): p-value > 1-gamma1

# Signal Log Ratio Algorithm
One-step Tukey's Biweight method