[BioC] Nimblegen and Ringo package

[Todd Richmond]

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
Madison, WI 53711
1-608-218-7600