mirna102Xgaincdf package

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Xiaobin Yuan ▴ 50

@xiaobin-yuan-4455

Last seen 10.2 years ago

Hi all, I have problem with the miRNA microarray from Affymetrix. I got the following error message: > data<-ReadAffy() > data AffyBatch object size of arrays=230x230 features (11 kb) cdf=miRNA-1_0_2Xgain (??? affyids) number of samples=5 Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain miRNA-1_0_2Xgain Library - package mirna102xgaincdf not installed Bioconductor - mirna102xgaincdf not available In addition: Warning message: missing cdf environment! in show(AffyBatch) I could not find a new package named "mirna102xgaincdf" from BioConductor. thanks Xiaobin Yuan [[alternative HTML version deleted]]

miRNA Microarray cdf miRNA Microarray cdf • 1.6k views

ADD COMMENT • link updated 13.8 years ago by James W. MacDonald 67k • written 13.8 years ago by Xiaobin Yuan ▴ 50

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 3 days ago

United States

Hi Xiaobin Yuan, You don't say what OS you are using, so I have attached both the source and win binary packages. If you are on Mac OS, you will either need to get set up to install source packages, or get the guys in Seattle to build the binary for that OS. Best, Jim >>> Xiaobin Yuan <xiaobin.yuan at="" louisville.edu=""> wrote: > Hi all, > > I have problem with the miRNA microarray from Affymetrix. I got > the following error message: > >> data<-ReadAffy() >> data > AffyBatch object > size of arrays=230x230 features (11 kb) > cdf=miRNA-1_0_2Xgain (??? affyids) > number of samples=5 > Error in getCdfInfo(object) : > Could not obtain CDF environment, problems encountered: > Specified environment does not contain miRNA-1_0_2Xgain > Library - package mirna102xgaincdf not installed > Bioconductor - mirna102xgaincdf not available > In addition: Warning message: > missing cdf environment! in show(AffyBatch) > > I could not find a new package named "mirna102xgaincdf" from > BioConductor. > > thanks > > Xiaobin Yuan > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

ADD COMMENT • link 13.8 years ago James W. MacDonald 67k

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Guido Hooiveld ★ 4.1k

@guido-hooiveld-2020

Last seen 2 days ago

Wageningen University, Wageningen, the …

Hi Xiaobin, Please keep this conversation on the list. No, the files you can download from Affymetrix are not an R-package; your really need a CDF environment for use in R. Ideally, the BioC core team will provide the R-version of this file, but for now I would suggest you specifically set the CDF environment as described here: http://thread.gmane.org/gmane.science.biology.informatics.conductor/32 287 Thus, pointing R into the data dir, and then: affy.data <- ReadAffy(cdfname="mirna10") Be sure, however, to have these package installed: source("http://www.bioconductor.org/biocLite.R") biocLite("mirna10cdf", "mirna10probe") HTH, Guido From: Xiaobin Yuan [mailto:xiaobin.yuan@louisville.edu] Sent: Friday, January 28, 2011 20:56 To: Hooiveld, Guido Subject: RE: [BioC] mirna102Xgaincdf package Hi Guido, Thanks for you reply. I downloaded file from : http://www.affymetrix.com/support/downloads/library_files/miRNA- 1_0_2xgain.zip. Can this file be treated as a R package. I ran the set up but was told that some files are missing. It looks that this file is designed for other software not for R. thanks Xiaobin >>> "Hooiveld, Guido" <guido.hooiveld@wur.nl<mailto:guido.hooiveld@wur.nl>> 1/28/2011 1:59 PM >>> Hi Xiaobin, Please see this thread: http://article.gmane.org/gmane.science.biology.informatics.conductor/3 2287 and all (4) posts/replies therein. HTH, Guido ------------------------------------------------ Guido Hooiveld, PhD Nutrition, Metabolism & Genomics Group Division of Human Nutrition Wageningen University Biotechnion, Bomenweg 2 NL-6703 HD Wageningen the Netherlands tel: (+)31 317 485788 fax: (+)31 317 483342 email: guido.hooiveld@wur.nl<mailto:guido.hooiveld@wur.nl> internet: http://nutrigene.4t.com http://www.researcherid.com/rid/F-4912-2010 -----Original Message----- From: bioconductor-bounces@r-project.org [mailto:bioconductor- bounces@r-project.org] On Behalf Of Xiaobin Yuan Sent: Friday, January 28, 2011 18:11 To: bioconductor@r-project.org Subject: [BioC] mirna102Xgaincdf package Hi all, I have problem with the miRNA microarray from Affymetrix. I got the following error message: > data<-ReadAffy() > data AffyBatch object size of arrays=230x230 features (11 kb) cdf=miRNA-1_0_2Xgain (??? affyids) number of samples=5 Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain miRNA-1_0_2Xgain Library - package mirna102xgaincdf not installed Bioconductor - mirna102xgaincdf not available In addition: Warning message: missing cdf environment! in show(AffyBatch) I could not find a new package named "mirna102xgaincdf" from BioConductor. thanks Xiaobin Yuan [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor@r-project.org<mailto:bioconductor@r-project.org> https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]

ADD COMMENT • link 13.8 years ago Guido Hooiveld ★ 4.1k

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Hi Xiaobin, It sounds like you need a cdf package that is presently not supported yet (I will look into this). But in the meantime you should be able to easily generate one if you look at the vignette found in of the makecdfenv package. You can see it in the documentation here: http://www.bioconductor.org/help/bioc- views/release/bioc/html/makecdfenv.html Marc On 01/28/2011 02:37 PM, Hooiveld, Guido wrote: > Hi Xiaobin, > Please keep this conversation on the list. > No, the files you can download from Affymetrix are not an R-package; your really need a CDF environment for use in R. Ideally, the BioC core team will provide the R-version of this file, but for now I would suggest you specifically set the CDF environment as described here: > http://thread.gmane.org/gmane.science.biology.informatics.conductor/ 32287 > Thus, pointing R into the data dir, and then: > affy.data <- ReadAffy(cdfname="mirna10") > Be sure, however, to have these package installed: > source("http://www.bioconductor.org/biocLite.R") > biocLite("mirna10cdf", "mirna10probe") > > HTH, > Guido > > From: Xiaobin Yuan [mailto:xiaobin.yuan at louisville.edu] > Sent: Friday, January 28, 2011 20:56 > To: Hooiveld, Guido > Subject: RE: [BioC] mirna102Xgaincdf package > > Hi Guido, > > Thanks for you reply. I downloaded file from : > http://www.affymetrix.com/support/downloads/library_files/miRNA- 1_0_2xgain.zip. > > Can this file be treated as a R package. I ran the set up but was told that some files are missing. It looks that this file is designed for other software not for R. > > thanks > Xiaobin > > > > >>>> "Hooiveld, Guido" <guido.hooiveld at="" wur.nl<mailto:guido.hooiveld="" at="" wur.nl="">> 1/28/2011 1:59 PM >>> >>>> > Hi Xiaobin, > Please see this thread: > http://article.gmane.org/gmane.science.biology.informatics.conductor /32287 > and all (4) posts/replies therein. > > HTH, > Guido > > ------------------------------------------------ > Guido Hooiveld, PhD > Nutrition, Metabolism & Genomics Group > Division of Human Nutrition > Wageningen University > Biotechnion, Bomenweg 2 > NL-6703 HD Wageningen > the Netherlands > tel: (+)31 317 485788 > fax: (+)31 317 483342 > email: guido.hooiveld at wur.nl<mailto:guido.hooiveld at="" wur.nl=""> > internet: http://nutrigene.4t.com > http://www.researcherid.com/rid/F-4912-2010 > > > > -----Original Message----- > From: bioconductor-bounces at r-project.org [mailto:bioconductor- bounces at r-project.org] On Behalf Of Xiaobin Yuan > Sent: Friday, January 28, 2011 18:11 > To: bioconductor at r-project.org > Subject: [BioC] mirna102Xgaincdf package > > Hi all, > > I have problem with the miRNA microarray from Affymetrix. I got > the following error message: > > >> data<-ReadAffy() >> data >> > AffyBatch object > size of arrays=230x230 features (11 kb) > cdf=miRNA-1_0_2Xgain (??? affyids) > number of samples=5 > Error in getCdfInfo(object) : > Could not obtain CDF environment, problems encountered: > Specified environment does not contain miRNA-1_0_2Xgain Library - package mirna102xgaincdf not installed Bioconductor - mirna102xgaincdf not available In addition: Warning message: > missing cdf environment! in show(AffyBatch) > > I could not find a new package named "mirna102xgaincdf" from BioConductor. > > thanks > > Xiaobin Yuan > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org<mailto:bioconductor at="" r-project.org=""> > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >

ADD REPLY • link 13.8 years ago Marc Carlson ★ 7.2k

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Hi Marc, Guido and Jim, After installing the packages you recommended or sent to me, now I can read the cel file to R. Thank very much for your help. Xiaobin >>> Marc Carlson <mcarlson@fhcrc.org> 1/28/2011 7:21 PM >>> Hi Xiaobin, It sounds like you need a cdf package that is presently not supported yet (I will look into this). But in the meantime you should be able to easily generate one if you look at the vignette found in of the makecdfenv package. You can see it in the documentation here: http://www.bioconductor.org/help/bioc- views/release/bioc/html/makecdfenv.html Marc On 01/28/2011 02:37 PM, Hooiveld, Guido wrote: > Hi Xiaobin, > Please keep this conversation on the list. > No, the files you can download from Affymetrix are not an R-package; your really need a CDF environment for use in R. Ideally, the BioC core team will provide the R-version of this file, but for now I would suggest you specifically set the CDF environment as described here: > http://thread.gmane.org/gmane.science.biology.informatics.conductor/32 287 > Thus, pointing R into the data dir, and then: > affy.data <- ReadAffy(cdfname="mirna10") > Be sure, however, to have these package installed: > source("http://www.bioconductor.org/biocLite.R") > biocLite("mirna10cdf", "mirna10probe") > > HTH, > Guido > > From: Xiaobin Yuan [mailto:xiaobin.yuan@louisville.edu] > Sent: Friday, January 28, 2011 20:56 > To: Hooiveld, Guido > Subject: RE: [BioC] mirna102Xgaincdf package > > Hi Guido, > > Thanks for you reply. I downloaded file from : > http://www.affymetrix.com/support/downloads/library_files/miRNA- 1_0_2xgain.zip. > > Can this file be treated as a R package. I ran the set up but was told that some files are missing. It looks that this file is designed for other software not for R. > > thanks > Xiaobin > > > > >>>> "Hooiveld, Guido" <guido.hooiveld@wur.nl<mailto:guido.hooiveld@wur.nl>> 1/28/2011 1:59 PM >>> >>>> > Hi Xiaobin, > Please see this thread: > http://article.gmane.org/gmane.science.biology.informatics.conductor/3 2287 > and all (4) posts/replies therein. > > HTH, > Guido > > ------------------------------------------------ > Guido Hooiveld, PhD > Nutrition, Metabolism & Genomics Group > Division of Human Nutrition > Wageningen University > Biotechnion, Bomenweg 2 > NL-6703 HD Wageningen > the Netherlands > tel: (+)31 317 485788 > fax: (+)31 317 483342 > email: guido.hooiveld@wur.nl<mailto:guido.hooiveld@wur.nl> > internet: http://nutrigene.4t.com > http://www.researcherid.com/rid/F-4912-2010 > > > > -----Original Message----- > From: bioconductor-bounces@r-project.org [mailto:bioconductor-bounces@r-project.org] On Behalf Of Xiaobin Yuan > Sent: Friday, January 28, 2011 18:11 > To: bioconductor@r-project.org > Subject: [BioC] mirna102Xgaincdf package > > Hi all, > > I have problem with the miRNA microarray from Affymetrix. I got > the following error message: > > >> data<-ReadAffy() >> data >> > AffyBatch object > size of arrays=230x230 features (11 kb) > cdf=miRNA-1_0_2Xgain (??? affyids) > number of samples=5 > Error in getCdfInfo(object) : > Could not obtain CDF environment, problems encountered: > Specified environment does not contain miRNA-1_0_2Xgain Library - package mirna102xgaincdf not installed Bioconductor - mirna102xgaincdf not available In addition: Warning message: > missing cdf environment! in show(AffyBatch) > > I could not find a new package named "mirna102xgaincdf" from BioConductor. > > thanks > > Xiaobin Yuan > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org<mailto:bioconductor@r-project.org> > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > _______________________________________________ Bioconductor mailing list Bioconductor@r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]

ADD REPLY • link 13.8 years ago Xiaobin Yuan ▴ 50

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