[BioC] RMA background adjustment for the Nimblegen array?

[Benilton Carvalho]

not hack is needed if you're using the oligo package... you'd need:

- XYS files provided by NimbleGen
- a data package specific to the array you're working with (built via  
makePlatformDesign)

Then,

library(oligo)
x=read.xysfiles(list.xysfiles())
y=rma(x)

The following might be useful:

http://www.bioconductor.org/workshops/2006/BioC2006/labs/bcarvalho/  
tutorial-slides.pdf

Please, let me know if you need more help (the packages are not  
documented yet, but i'm working on this).

b

On Feb 28, 2007, at 12:31 PM, Khan, Sohail wrote:

> 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
>
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