[Module Description]

Sample quality

• Sample prep controls
• 3'/5' for control genes
• RNA degradation plot

Hybridization quality

• Spike-in controls
• Background intensity
• Percent present
• PMA calls table
• Pos/Neg controls
• Affx control profiles

Signal comparability

• Scale factor
• Boxplot
• Density histogram

• MA plots

• Reference Layout
• Pos/Neg COI plot
• 2D spatial images

• NUSE plot
• RLE plot

Array correlation

• Correlation plot
• PCA analysis
• Clustering