[BioC] Nimblegen and Ringo package

[Joern Toedling]

Hello João,

João Fadista wrote:
> 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? 
>   

I am not totally sure if it is still the case, but NimbleGen have used
the tukey-biweight scaling to produce the data *.gff files from the
scanned two-channel intensities.
See http://www.nimblegen.com/products/chip/index.html
and scroll down to the FAQ and show all topics. Various manuals mention
it as well. I did not find this scaling terribly useful and did mainly
include if for sake of completeness.

>  
> 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. 
>   

Yes, there is. Have a look in the scripts directory of the installed
Ringo package. In there you will find an R script called
"makeProbeAnno.R" that shows how to produce a probeAnno environment from
NimbleGen's POS files. Please get back to me, if you encounter any
problems with this script. I would also suggest to download and install
the current development version of Ringo (version > 1.1.8) from the
Bioconductor web site at
http://www.bioconductor.org/packages/2.1/bioc/html/Ringo.html
since I streamlined that script considerably after the original release.

Best regards,
Joern

-- 
Joern Toedling
EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD
United Kingdom
Phone  +44(0)1223 492566
Email  toedling at ebi.ac.uk