[BioC] Nimblegen and Ringo package
Joao.Fadista at agrsci.dk
Thu Aug 16 16:48:51 CEST 2007
Hi Joern and Todd,
Thanks for the replies. Indeed, after the reply from Joern I found in the Nimblegen website that the the qspline is for normalizing CGH data while the tukey.biweight is for scaling ChIP-chip data.
I am analysing the demo Nimblegen CGH data with Ringo package because I think is the only bioconductor package that can convert the .pair raw files from nimblegen into RGList, right? After I get the RGList then I can use the packages suitable for CGH analysis.
By the way, I came up with another question. As I read through the CGH NimbleScan User´s Guide I didn´t find a file that describes the statistics of the fluorescent spots for each probe, like the GenePix software does (SD of the pixel intensity, Signal to noise ratio, a score for each spot, etc.). Can you generate that kind of files? If not, is it possible to transform a .ndf into a .gal file (http://www.moleculardevices.com/pages/software/gn_genepix_file_formats.html#gal) in order to be able to analyse the nimblegen .tiff images in GenePix?
From: Todd Richmond [mailto:todd at nimblegen.com]
Sent: Thursday, August 16, 2007 3:53 PM
To: João Fadista; bioconductor at stat.math.ethz.ch
Subject: RE: [BioC] Nimblegen and Ringo package
NimbleGen does use the qspline method (normalize.qspline from the affy package) for normalizing CGH data. The tukey.biweight mean is used to scale ChIP-chip ratio gff files so that the data is centered on zero. We do not use qspline, or indeed any other normalization method, for ChIP-chip data, since we have not found a method that does not adversely affect downstream data quality.
Since Ringo is a package for analyzing ChIP-chip data, I'm assuming that's why that's there. I'm curious, though, why you are trying to use it for CGH data, when there are a number of other packages specifically mean for CGH analysis.
> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor-
> bounces at stat.math.ethz.ch] On Behalf Of João Fadista
> Sent: Thursday, August 16, 2007 2:46 AM
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] Nimblegen and Ringo package
> 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
> UNIVERSITY OF AARHUS
> Faculty of Agricultural Sciences
> Dept. of Genetics and Biotechnology
> Blichers Allé 20, P.O. BOX 50
> DK-8830 Tjele
> Phone: +45 8999 1900
> Direct: +45 8999 1900
> E-mail: Joao.Fadista at agrsci.dk <mailto:Joao.Fadista at agrsci.dk>
> Web: www.agrsci.org <http://www.agrsci.org/>
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