Sources of
Systematic Errors (bias)
ØDifferent incorporation efficiency of dyes
ØDifferent amounts of mRNA
ØExperimenter/protocol issues (comparing chips processed by different labs)
ØDifferent scanning
parameters
ØBatch bias
lIdeally: scatter plot coincides with the x=y diagonal
¡VDue to Random errors:
we expect to see a ¡¥cloud¡¦ around the x=y diagonal.
lIn practice: Both Random and Systematic measurement errors (Bias)
¡VDue to Biases scatter
plots are not centered around the x-y diagonal
Hybridization of the same sample to 2 chips/channels