Dear all,
 
I am using the Ringo package to analyse some demo CGH data from Nimblegen (ftp://ftp.nimblegen.com/pub/demo_data/). 
 
1 - In the NimbleScan User´s Guide version 2.3 it is written that they use the qspline normalization method (Christopher Workman, et al. "A new non-linear normalization method for reducing variability in dna microarray experiments". Genome Biology 2002) which I believe is the one implemented in the affy package, right? Despite of this, the Ringo package has a supposed nimblegen normalization method related to the tukey.biweight function also appearing in the affy package.
Maybe I am wrong, but why did the Ringo package named a supposed nimblegen normalization method to a method which as far as I know is not from nimblegen? 
 
2 - Another question is related to the probeAnno.rda file which is needed in some function implemented in the Ringo package. Since I don´t have these kind of files I was wondering if I have the start/end positions and the indices of the probes is there any easy way to make the probeAnno.rda files? P.S. If it helps, In the demo data I have .pos, .ndf, .pair and .gff files. 
 
 


Best regards

João Fadista
Ph.d. student


 	
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