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

[Ernest Turro]

Hi Rainer,

FYI there's a new version of bgx called mmbgx, available from http://bgx.org.uk 
  (though not in bioconductor yet), which works with Gene ST arrays.

Regards,
Ernest

On 15 Jun 2010, at 12:35, "Groot, Philip de" <philip.degroot at wur.nl>  
wrote:

> 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
> PO Box 8129, 6700 EV Wageningen
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> Dreijenweg 2, 6703 HA  Wageningen
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> E-mail:   Philip.deGroot at wur.nl
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>             http://humannutrition.wur.nl/
>             https://madmax.bioinformatics.nl/
> ________________________________________
> 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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