[BioC] Nimblegen and Ringo package

[João Fadista]

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?


Best regards,
João Fadista





-----Original Message-----
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


Hi João,

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.

Todd

> -----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/>


--
Todd Richmond
NimbleGen Systems, Inc.
Manager of Research Informatics
One Science Court
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