[BioC] gc-rma and vsn normalization for rat microarray data

[Groot, Philip de]

Hello Rainer,

Why don't you simply use vsnrma? This works perfectly fine for Gene ST arrays!
This function resides in the vsn library.

Regards,

Dr. Philip de Groot Ph.D.
Bioinformatics Researcher

Wageningen University / TIFN
Nutrigenomics Consortium
Nutrition, Metabolism & Genomics Group
Division of Human Nutrition
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________________________________________
From: Richard Pearson [richard.pearson at well.ox.ac.uk]
Sent: 14 June 2010 15:08
To: Rainer Tischler
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] gc-rma and vsn normalization for rat microarray data

Rainer

Unfortunately you're not going to be able to use puma as the methods require both perfect
match (PM) and mismatch (MM) data (and exon arrays have only the PM).

Best wishes

Richard

Benilton Carvalho wrote:
> Rainer,
>
> I understand I don't offer a vsn() method in oligo (yet), but this can
> be easily achieved... Something like the following may get you
> started:
>
> library(oligo)
> cels = list.celfiles()
> raw = read.celfiles(cels)
> pms = pm(raw)
> pmsVSN = vsn::vsnMatrix(pms)
> pm(raw) <- pmVSN
> rm(pms, pmsVSN)
>
> If any of the other packages offer you a way of normalizing the data
> straight from the PM matrices, you can do as I show above...
>
> b
>
>
> On 11 June 2010 16:20, Rainer Tischler <rainer_t62 at yahoo.de> wrote:
>> Dear all,
>>
>> I am analyzing microarray data from an Affymetrix GeneChip Rat ST 1.0 platform, however, since there is no annotation package available that is compatible with the R-package "affy", so far I have only been able to normalize the data using the simple RMA method from the oligo-package. I would like to apply more advanced normalization methods like GC-RMA, VSN, PUMA or BGX, but none of these methods seems to be compatible with the oligo-package.
>> Is anybody aware of a possibility to analyze Affymetrix Rat data with the standard affy-package, or alternatively, a possibility to use any of the above normalization methods with the oligo-package?
>>
>> Many thanks,
>> Rainer
>>
>>
>>
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>
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--
Dr Richard D Pearson                       richard.pearson at well.ox.ac.uk
Wellcome Trust Centre for Human Genetics   http://www.well.ox.ac.uk/~rpearson
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