BioC packages for Human Gene 1.0 ST arrays
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jiayu wen ▴ 60
@jiayu-wen-3573
Last seen 8.2 years ago
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@groot-philip-de-1307
Last seen 8.2 years ago
Hello Jean, You can use the same packages if you use hugene10stv1.r3cdf <http: bi="" oconductor.org="" packages="" 2.5="" data="" annotation="" html="" hugene10stv1.r3cdf.ht="" ml=""> . Loading the .CEL-files is done as follows: x <- ReadAffy(cdfname="hugene10stv1.r3cdf <http: bioconductor.org="" pac="" kages="" 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@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 [[alternative HTML version deleted]]
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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="" p="" ackages="" 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 > [[alternative HTML version deleted]] > > > > >
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