[BioC] Normalization of 2 color Nimblegen array

dhruv k pant dhruv.cshl.work at gmail.com
Fri Jun 8 04:20:32 CEST 2007

Rafael A. Irizarry <ririzarr at ...> writes:

> Hi! I just wanted to point out that the oligo package supports nimblegen
> arrays (you need the xys and ndf) files. It is under development but we 
> need testers. If anybody wants a specific method or function 
> incorporated you can email benitlon or me. Most functions in the affy 
> package can be easily exproted.
> -r

Hi Rafael,

I was wondering if the affyPLM function fitPLM (which takes an affybatch object)
could be applied to Nimblegen ftr(xys) files. I have the ndf file and using  the
library makePlatformDesign, I've created the appropriate package.

The oligo function read.xysfiles creates an ExpressionFeatureSet object which is
incompatible for fitPLM.

I've tried to convert the ftr files to Affy CEL file format, in which case I
could use function ReadAffy to create an AffyBatch object. but presumably the
NDF file also has to converted to CDF format??


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