Hi,

I am given 8 oligo arrays, and hope to use limma package to process their
gpr files.

            R              G
GPR 1: Treated     Ref
GPR 2: Ref           Treated
 GPR 3: Control     Ref
GPR 4: Ref          Control

GPR 5 to 8 are the same as GPR 1 to 4, except that the former is generated
from a different cell line.

Couple of question as to the suitability of
a) Background correction method
b) NormalizeWithinArrays method
c) normalizeBetweenArrays method, should this be applied to GPR 1 to 4, or
GPR 1 to 8 ?

In addition,
A) what should the design matrix be ?
B) Is lmfit required ?

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