# Applying analysis routes on the Ag Spike dataset 
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# Note: The scripts were run using R 2.7.2.
#
# citation: "A wholly-defined Agilent microarray spike-in dataset" Qianqian Zhu; Jeffrey C. Miecznikowski; Marc S. Halfon Bioinformatics 2011; doi: 10.1093/bioinformatics/btr135
#
# Qianqian Zhu, 3/2011

R --no-save < readAgilent.R # load the Ag Spike dataset and save as a R object
R --no-save < pre-processing.R # background correction, within-array normalization, between-array normalization 
R --no-save < FeatureExtraction.R # read the processed intensities of Feature Extraction Software
R --no-save < DEGtest.R # test for DEGs
R --no-save < DEGAUC.R # calculate partial AUC values

