CDF for Cytogenetics_Array
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Lenka Radova ▴ 40
@lenka-radova-4046
Last seen 9.7 years ago
Hi, I have a problem with new Cytogenetics Array from Affymetrix. I have original Affy .cdf file from web, but I´m not able to create a cdf- package using make.cdf.package. Thanks for any help. Lenka [[alternative HTML version deleted]]
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@wolfgang-huber-3550
Last seen 25 days ago
EMBL European Molecular Biology Laborat…
Lenka Radova scripsit 27/04/10 13:28: > Hi, > I have a problem with new Cytogenetics Array from Affymetrix. I have > original Affy .cdf file from web, but I?m not able to create a cdf- package > using make.cdf.package. > Thanks for any help. Lenka Dear Lenka you will increase your chances of getting a useful answer by asking a useful question. You might have a look at the posting guide http://www.bioconductor.org/docs/postingGuide.html in order to find out how to do so. One particularly important point is: "If possible, send a simple and reproducible example along with the output of sessionInfo(). If the example produces an error, also provide the error message and the output of traceback()." Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber
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Using the oligo package, you can import the data from the Cytogenetics arrays (it should be able to download/install the required annotation package, but you can download it directly from http://www.bioconductor.org/packages/release/data/annotation/html/pd.c ytogenetics.array.html ). I don't have any workflow specific for the cyto chip yet, but this should suffice for you to import data and use it in combination with other BioC packages that you may find relevant. b On Tue, Apr 27, 2010 at 12:39 PM, Wolfgang Huber <whuber at="" embl.de=""> wrote: > Lenka Radova scripsit 27/04/10 13:28: >> >> Hi, >> I have a problem with new Cytogenetics Array from Affymetrix. I have >> original Affy .cdf file from web, but I?m not able to create a cdf- package >> using make.cdf.package. >> Thanks for any help. Lenka > > Dear Lenka > > you will increase your chances of getting a useful answer by asking a useful > question. You might have a look at the posting guide > http://www.bioconductor.org/docs/postingGuide.html > in order to find out how to do so. > > One particularly important point is: > "If possible, send a simple and reproducible example along with the output > of sessionInfo(). If the example produces an error, also provide the error > message and the output of traceback()." > > Wolfgang Huber > EMBL > http://www.embl.de/research/units/genome_biology/huber > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
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Hi, I have the original cdf file from Affymetrix web page (Cytogenetics_Array.CDF) in my working directory and I tried the following... Lenka > library(makecdfenv) > make.cdf.package("Cytogenetics_Array.cdf", cdf.path = getwd(), compress = FALSE, species = "Homo_sapiens") Error in make.cdf.env(filename, cdf.path = cdf.path, compress = compress, : makecdfenv does not currently know how to handle cdf files of this type (genotyping). > sessionInfo() R version 2.10.0 (2009-10-26) i386-pc-mingw32 locale: [1] LC_COLLATE=Czech_Czech Republic.1250 LC_CTYPE=Czech_Czech Republic.1250 [3] LC_MONETARY=Czech_Czech Republic.1250 LC_NUMERIC=C [5] LC_TIME=Czech_Czech Republic.1250 attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] makecdfenv_1.24.0 affyio_1.14.0 affy_1.24.2 Biobase_2.6.1 loaded via a namespace (and not attached): [1] preprocessCore_1.8.0 [[alternative HTML version deleted]]
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On Tue, Apr 27, 2010 at 8:03 AM, Lenka Radova <avodar at="" gmail.com=""> wrote: > Hi, > I have the original cdf file from Affymetrix web page > (Cytogenetics_Array.CDF) ?in my working directory and I tried the > following... Lenka > >> library(makecdfenv) > >> ?make.cdf.package("Cytogenetics_Array.cdf", cdf.path = getwd(), compress = > FALSE, species = "Homo_sapiens") > Error in make.cdf.env(filename, cdf.path = cdf.path, compress = compress, ?: > > ?makecdfenv does not currently know how to handle cdf files of this type > (genotyping). Hi, Lenka. You'll want to use the oligo package, as Benilton suggested, to process this chip type. make.cdf.env is for 3' biased gene expression arrays only, really. Sean >> sessionInfo() > R version 2.10.0 (2009-10-26) > i386-pc-mingw32 > locale: > [1] LC_COLLATE=Czech_Czech Republic.1250 ?LC_CTYPE=Czech_Czech > Republic.1250 > [3] LC_MONETARY=Czech_Czech Republic.1250 > LC_NUMERIC=C > [5] LC_TIME=Czech_Czech Republic.1250 > attached base packages: > [1] tools ? ? stats ? ? graphics ?grDevices utils ? ? datasets ?methods > [8] base > other attached packages: > [1] makecdfenv_1.24.0 affyio_1.14.0 ? ? affy_1.24.2 ? ? ? Biobase_2.6.1 > loaded via a namespace (and not attached): > [1] preprocessCore_1.8.0 > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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Thanks a lot. The oligo package works. Lenka 2010/4/27 Sean Davis <seandavi@gmail.com> > On Tue, Apr 27, 2010 at 8:03 AM, Lenka Radova <avodar@gmail.com> wrote: > > Hi, > > I have the original cdf file from Affymetrix web page > > (Cytogenetics_Array.CDF) in my working directory and I tried the > > following... Lenka > > > >> library(makecdfenv) > > > >> make.cdf.package("Cytogenetics_Array.cdf", cdf.path = getwd(), compress > = > > FALSE, species = "Homo_sapiens") > > Error in make.cdf.env(filename, cdf.path = cdf.path, compress = compress, > : > > > > makecdfenv does not currently know how to handle cdf files of this type > > (genotyping). > > Hi, Lenka. > > You'll want to use the oligo package, as Benilton suggested, to > process this chip type. make.cdf.env is for 3' biased gene expression > arrays only, really. > > Sean > > >> sessionInfo() > > R version 2.10.0 (2009-10-26) > > i386-pc-mingw32 > > locale: > > [1] LC_COLLATE=Czech_Czech Republic.1250 LC_CTYPE=Czech_Czech > > Republic.1250 > > [3] LC_MONETARY=Czech_Czech Republic.1250 > > LC_NUMERIC=C > > [5] LC_TIME=Czech_Czech Republic.1250 > > attached base packages: > > [1] tools stats graphics grDevices utils datasets methods > > [8] base > > other attached packages: > > [1] makecdfenv_1.24.0 affyio_1.14.0 affy_1.24.2 Biobase_2.6.1 > > loaded via a namespace (and not attached): > > [1] preprocessCore_1.8.0 > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > [[alternative HTML version deleted]]
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@wolfgang-huber-3550
Last seen 25 days ago
EMBL European Molecular Biology Laborat…
OK - so in this case a useful answer was obtained without following the posting guide. Thanks, Benilton ! :) > Using the oligo package, you can import the data from the Cytogenetics > arrays (it should be able to download/install the required annotation > package, but you can download it directly from > http://www.bioconductor.org/packages/release/data/annotation/html/pd .cytogenetics.array.html > ). > > I don't have any workflow specific for the cyto chip yet, but this > should suffice for you to import data and use it in combination with > other BioC packages that you may find relevant. > > b > > On Tue, Apr 27, 2010 at 12:39 PM, Wolfgang Huber <whuber at="" embl.de=""> wrote: >> Lenka Radova scripsit 27/04/10 13:28: >>> >>> Hi, >>> I have a problem with new Cytogenetics Array from Affymetrix. I have >>> original Affy .cdf file from web, but I?m not able to create a cdf-package >>> using make.cdf.package. >>> Thanks for any help. Lenka >> >> Dear Lenka >> >> you will increase your chances of getting a useful answer by asking a useful >> question. You might have a look at the posting guide >> http://www.bioconductor.org/docs/postingGuide.html >> in order to find out how to do so. >> >> One particularly important point is: >> "If possible, send a simple and reproducible example along with the output >> of sessionInfo(). If the example produces an error, also provide the error >> message and the output of traceback()." >> >> Wolfgang Huber >> EMBL >> http://www.embl.de/research/units/genome_biology/huber >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >>
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