[BioC] RMA background adjustment for the Nimblegen array?

[Todd Richmond]

Khan, Sohail wrote:
> Drear All,
> 
> Is it appropriate to apply the "rma" background adjustment to the
Nimblegen arrays?

I should hope so - we apply it to all of the expression data that we 
process and ship to customers. :)

> Can it be done by hacking the rma code? 

As Benilton pointed out, the easiest way to use rma on your expression 
data (if you are not a service customer) is to use the oligo package.

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. >

The background in this case is the non-specific binding, not an 
image-based background correction. The experimental features on most 
NimbleGen arrays  are arranged in checkboard fashion, meaning that there 
is an empty feature on all four sides of every experimental feature. 
However given the size of the features (16 microns) and a standard 5 
micron scanner, features are only 3x3 pixels. Since there is some amount 
of signal bleed-over you would want to ignore a 1 pixel border in the 
empty features, leaving you with 4 pixels of background information that 
you would want to use. With a higher resolution scanner, you have more 
pixels to play with, and image-based background correction is probably 
more feasible.

Todd



-- 
Todd Richmond, PhD
Manager of Research Informatics
NimbleGen Systems, Inc
Madison, WI 53719
1-608-218-7600