[BioC] RMA background adjustment for the Nimblegen array?

[Khan, Sohail]

Drear All,

Is it appropriate to apply the "rma" background adjustment to the Nimblegen arrays?  Can it be done by hacking the rma code? The background is the background intensity around the features or is it the non-specific binding? As I understand it, the features on the Nimblegen arrays are next to each other (no gaps).  In addition, it has probably been asked many times.  What is the background correction method for the rma algorithm (in simple terms)?
Thanks for your expert advice.


Sohail Khan
Scientific Programmer
COLD SPRING HARBOR LABORATORY
Genome Research Center
500 Sunnyside Boulevard
Woodbury, NY 11797
(516)422-4076