Array level quality control

•Problems:

–array fabrication defect

–problem with RNA extraction

–failed labeling reaction

–poor hybridization conditions

–faulty scanner

–

•Quality measures:

–Percentage of spots with no signal (~30% excluded spots)

–Range of intensities

–(Av. Foreground)/(Av. Background) > 3 in both channels

–Distribution of spot signal area

–Amount of adjustment needed: signals have to substantially changed to make slides comparable.