Question regarding the R data package.....???

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arun kumar vinnakota ▴ 30

@arun-kumar-vinnakota-120

Last seen 10.3 years ago

Hi, I am a grad student in University of newmexico and i am working with R program but i am unable to read the R data package "Enzyme2affy" inthe bionconductor . Basically i need the EC numbers of all the affymetrix chip RatU34a. Plz let me know what i need to do and do i need to use the annotate or annbuilder package to read the "Enzyme2affy" R data package. Sincerely, Arun

annotate AnnBuilder annotate AnnBuilder • 1.1k views

ADD COMMENT • link updated 21.8 years ago by John Zhang ★ 2.9k • written 21.8 years ago by arun kumar vinnakota ▴ 30

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John Zhang ★ 2.9k

@john-zhang-6

Last seen 10.3 years ago

Here is the R code to do that (assuming you have alread installed rgu34a): library(rgu34a) library(Biobase) enzymeNAffy <- multiget(ls(rgu34aENZYME2AFFY), rgu34aENZYME2AFFY) >To: bioconductor@stat.math.ethz.ch >From: arun kumar vinnakota <arun@unm.edu> >MIME-Version: 1.0 >Content-Transfer-Encoding: 8bit >X-Originating-IP: 129.24.128.102 >X-Virus-Scanned: by amavisd-milter (http://amavis.org/) >X-Virus-Scanned: by amavisd-milter (http://amavis.org/) >X-Spam-Status: No, hits=0.8 required=5.0 tests=SPAM_PHRASE_00_01 version=2.43 >X-Spam-Level: >Subject: [BioC] Question regarding the R data package.....??? >X-BeenThere: bioconductor@stat.math.ethz.ch >X-Mailman-Version: 2.0.13 >List-Help: <mailto:bioconductor- request@stat.math.ethz.ch?subject="help"> >List-Post: <mailto:bioconductor@stat.math.ethz.ch> >List-Subscribe: <http: www.stat.math.ethz.ch="" mailman="" listinfo="" bioconductor="">, <mailto:bioconductor-request@stat.math.ethz.ch?subject=subscribe> >List-Id: The Bioconductor Project Mailing List <bioconductor.stat.math.ethz.ch> >List-Unsubscribe: <http: www.stat.math.ethz.ch="" mailman="" listinfo="" bioconductor="">, <mailto:bioconductor-request@stat.math.ethz.ch?subject=unsubscribe> >List-Archive: <http: www.stat.math.ethz.ch="" pipermail="" bioconductor=""/> >Date: Mon, 03 Mar 2003 09:19:19 -0700 > > Hi, > I am a grad student in University of newmexico and i am working >with R program but i am unable to read the R data package "Enzyme2affy" >inthe bionconductor . Basically i need the EC numbers of all the >affymetrix chip RatU34a. Plz let me know what i need to do and do i >need to use the annotate or annbuilder package to read >the "Enzyme2affy" R data package. >Sincerely, >Arun > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor Jianhua Zhang Department of Biostatistics Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084

ADD COMMENT • link 21.8 years ago John Zhang ★ 2.9k

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> > library(rgu34a) > library(Biobase) > enzymeNAffy <- multiget(ls(rgu34aENZYME2AFFY), rgu34aENZYME2AFFY) i am going to expand on the above answer a little bit... 1) You have to get the rgu34a data package from the Data Packages node of bioconductor. if you are using windows, get the zip file onto your hard drive and use the package tab on the gui to install the package from the zip file 2) once it is installed, library(rgu34a) will give you access to a collection of environments and documents. library(help=rgu34a) will give a catalog of resources 3) if you mention rgu34aENZYME2AFFY to the R interpreter you get a very brief response: the environment tag. 4) "ls" is a function that returns the names of entities collected in the environment given to it as argument. strictly speaking, the answer to your question comes from running unique on the unqualified ls(rgu34aENZYME2AFFY), that will give the list of all EC labels. what is provided by Jianhua is the list mapping from EC labels to vectors of affy probe ids. > > > > > Hi, > > I am a grad student in University of newmexico and i am working > >with R program but i am unable to read the R data package "Enzyme2affy" > >inthe bionconductor . Basically i need the EC numbers of all the > >affymetrix chip RatU34a. Plz let me know what i need to do and do i > >need to use the annotate or annbuilder package to read > >the "Enzyme2affy" R data package. > >Sincerely, > >Arun > > > >_______________________________________________ > >Bioconductor mailing list > >Bioconductor@stat.math.ethz.ch > >http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > Jianhua Zhang > Department of Biostatistics > Dana-Farber Cancer Institute > 44 Binney Street > Boston, MA 02115-6084 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >

ADD REPLY • link 21.8 years ago Vincent J. Carey, Jr. 6.7k

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Hi! I have two question regarding the invariant set method for normalization. First, is the algorithm the IDS described by Schadt et al. (2001)? With any further modifications? Second, what do the warnings below mean? Best, Hinnerk > HEP.invset <- express(HEP,normalize.method="invariantset") Background correcting Normalizing Data 12625 ProbeSets to be processed ......... Warning messages: 1: Collapsing to unique x values in: approx(tmp$n.curve$y, tmp$n.curve$x, xout = intensity(abatch)[, 2: Collapsing to unique x values in: approx(tmp$n.curve$y, tmp$n.curve$x, xout = intensity(abatch)[, 3: Collapsing to unique x values in: approx(tmp$n.curve$y, tmp$n.curve$x, xout = intensity(abatch)[,

ADD REPLY • link 21.8 years ago Hinnerk Boriss ▴ 220

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