Single Array Analysis (Oilgonucleotide expression arrays)

# Single stranded DNA, 25 bp

# 14~20 probe pairs for each gene

# Each probe pair has a Perfect Match (PM) and a Miss Match (MM)

# MAS 4.0 (Average difference) = average of PM-MM difference

# Low-level anaysis: feature extraction, normalization, computation of expression indexes

# High-level analysis: t-test, ANOVA

# Discrimination Score
R = (PM - MM) / (PM + MM)

# Detection p-value by One-sided Wilcoxon's Signed Rank test
H0: E(R) = tau (default = 0.015)
Ha: E(R) > tau

# Detection Call
Present: p-value <= alpha1
Marginal: alpha1 < p-value <= alpha2
Absent: p-value > alpha2

defaults: alpha1=0.04, alpha2 = 0.06

# Signal Algorithm
One-Step Turkey's Biweight Estiimate

If PM > MM, informative
if PM < MM, uninformative and use an imputed value called Idealized Mismatch (IM)