[BioC] BioC packages for Human Gene 1.0 ST arrays

[jiayu wen]

Hi Philip,

Thanks for your quick reply! I will try that then.

Regards,
Jean
On Apr 7, 2010, at 12:12 PM, Groot, Philip de wrote:

> Hello Jean,
>
> You can use the same packages if you use hugene10stv1.r3cdf <http://bioconductor.org/packages/2.5/data/annotation/html/hugene10stv1.r3cdf.html 
> > .
> Loading the .CEL-files is done as follows:
>
> x <- ReadAffy(cdfname="hugene10stv1.r3cdf <http://bioconductor.org/packages/2.5/data/annotation/html/hugene10stv1.r3cdf.html 
> > ")
>
> Alternatively, you can use the MBNI Custom CDF files which contain  
> remapped probes in newly defined probesets.
> More info: http://nugo-r.bioinformatics.nl/NuGO_R.html
>
> 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
> Visiting Address: Erfelijkheidsleer: De Valk, Building 304
> Dreijenweg 2, 6703 HA  Wageningen
> Room: 0052a
> T: +31-317-485786
> F: +31-317-483342
> E-mail:   Philip.deGroot at wur.nl <mailto:Philip.deGroot at wur.nl>
> Internet: http://www.nutrigenomicsconsortium.nl <http://www.nutrigenomicsconsortium.nl/ 
> >
>             http://humannutrition.wur.nl <http://humannutrition.wur.nl/ 
> >
>             https://madmax.bioinformatics.nl <https://madmax.bioinformatics.nl/ 
> >
>
>
>
>
> ________________________________
>
> From: jiayu wen [mailto:jiayu.jean.wen at gmail.com]
> Sent: Wed 7-4-2010 7:46
> To: bioconductor
> Subject: [BioC] BioC packages for Human Gene 1.0 ST arrays
>
>
>
> Dear list,
>
> I used ReadAffy, vsnrma, nsFilter, and Limma to analyze hgu133plus2
> arrays.
> What is the equivalent package to analyze Human Gene 1.0 ST arrays?
> Thanks.
>
> Jean
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