•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.