Question: phenodata - rtfm
0
16.9 years ago by
rgentleman5.5k
United States
rgentleman5.5k wrote:
On Wed, Jan 29, 2003 at 11:31:56AM +0100, Hinnerk Boriss wrote: > Hi there! > I am still having difficulties setting up the phenodata properly. > I did set up my data.frame like Wolfgang suggested to do it: > > chip.group <- rep(seq(1:4),each=3) > chip.group2 <- c("a","a","a","b","b","b","c","c","c","d","d","d") > contrasts1 <- c("T","T","T","F","F","F","T","T","T","F","F","F") > contrasts2 <- c("F","F","F","F","F","F","T","T","T","T","T","T") > chip.names=c("nC1","nC2","nC3","1h1","1h2","1h3","4h1","4h2","4h3"," C1", > "C2","C3") > annotation <- > data.frame(chip.group,chip.group2,chip.names,contrasts1,contrasts2) > pD <- new("phenoData", pData=annotation) > ExData@phenoData <- pD > Hi, There is a little more, first, class?exprSet gets you help on the class exprSet, in that you see that phenoData is a slot in that class that should take a value of class phenoData, The documentation is found using class?phenoData which says that these objects have two components, pData and varLabels, you only supplied one of them. Here is a simple example: data(geneData) data(geneCov) covdesc<- list("Covariate 1", "Covariate 2", "Covariate 3") names(covdesc) <- names(geneCov) pdata <- new("phenoData", pData=geneCov, varLabels=covdesc) so you have to make up the description of the variables, as a character vector of the right length; Robert > This works fine, except that the varLabels aren't set: > > > ExData.rma > Expression Set (exprSet) with > 12625 genes > 12 samples > phenoData object with 5 variables and 12 cases > varLabels > > > > and the covariate isn't used properly: > table(ExData.rma[["chip.group2"]]) > a b c d > 0 0 0 0 > > What is it that I am still doing wrong here? > > Best, > Hinnerk > > > -----Original Message----- > > From: bioconductor-admin@stat.math.ethz.ch > > [mailto:bioconductor-admin@stat.math.ethz.ch] On Behalf Of > > Wolfgang Huber > > Sent: Thursday, January 16, 2003 10:50 AM > > To: Hinnerk Boriss; 'Bioconductor' > > Subject: RE: [BioC] phenodata - rtfm > > > > > > Hi Hinnerk, > > > > It is simply a dataframe with as many rows (observations) as there are > > columns (chips/arrays) in the exprs matrix. You can populate > > it with data as > > you would populate any dataframe, and use the data in models > > and plots just > > as with any dataframe. > > > > Regards > > Wolfgang > > > > Division of Molecular Genome Analysis (Poustka Lab) > > German Cancer Research Center (DKFZ) > > Im Neuenheimer Feld 580 > > 69120 Heidelberg, Germany > > > > w.huber@dkfz.de > > http://www.dkfz.de/abt0840/whuber > > Tel +49-6221-424709 > > Fax +49-6221-42524709 > > > > > > -----Original Message----- > > From: bioconductor-admin@stat.math.ethz.ch > > [mailto:bioconductor-admin@stat.math.ethz.ch]On Behalf Of > > Hinnerk Boriss > > Sent: Thursday, January 16, 2003 10:02 AM > > To: 'Bioconductor' > > Subject: [BioC] phenodata > > > > > > Hi there, > > > > Can anyone tell me how to use the phenoData item. For one thing in a > > technical sense of how to populate the object with data. And > > also in the > > analysis sense, of how to use the data once they are there. In other > > words, is it possible use those data as factors in ANOVA or plots etc? > > > > Thanks for your help! > > > > Best, > > Hinnerk > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- +--------------------------------------------------------------------- ------+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20 | Harvard School of Public Health email: rgentlem@jimmy.dfci.harvard.edu | +--------------------------------------------------------------------- ------+
annotation cancer • 642 views
modified 16.9 years ago by Hinnerk Boriss220 • written 16.9 years ago by rgentleman5.5k
0
16.9 years ago by
Rafael A. Irizarry640 wrote:
you can also use the read.phenoData file which returns a phenoData instance. it reads flat files or uses widgets. -r On Wed, 29 Jan 2003, Robert Gentleman wrote: > On Wed, Jan 29, 2003 at 11:31:56AM +0100, Hinnerk Boriss wrote: > > Hi there! > > I am still having difficulties setting up the phenodata properly. > > I did set up my data.frame like Wolfgang suggested to do it: > > > > chip.group <- rep(seq(1:4),each=3) > > chip.group2 <- c("a","a","a","b","b","b","c","c","c","d","d","d") > > contrasts1 <- c("T","T","T","F","F","F","T","T","T","F","F","F") > > contrasts2 <- c("F","F","F","F","F","F","T","T","T","T","T","T") > > chip.names=c("nC1","nC2","nC3","1h1","1h2","1h3","4h1","4h2","4h3" ,"C1", > > "C2","C3") > > annotation <- > > data.frame(chip.group,chip.group2,chip.names,contrasts1,contrasts2) > > pD <- new("phenoData", pData=annotation) > > ExData@phenoData <- pD > > > > Hi, > There is a little more, > first, > class?exprSet > gets you help on the class exprSet, > in that you see that phenoData is a slot in that class that should > take a value of class phenoData, > > The documentation is found using > class?phenoData > > which says that these objects have two components, > pData and varLabels, > you only supplied one of them. > > Here is a simple example: > data(geneData) > data(geneCov) > covdesc<- list("Covariate 1", "Covariate 2", "Covariate 3") > names(covdesc) <- names(geneCov) > pdata <- new("phenoData", pData=geneCov, varLabels=covdesc) > > so you have to make up the description of the variables, as a > character vector of the right length; > > Robert > > > > > This works fine, except that the varLabels aren't set: > > > > > ExData.rma > > Expression Set (exprSet) with > > 12625 genes > > 12 samples > > phenoData object with 5 variables and 12 cases > > varLabels > > > > > > > and the covariate isn't used properly: > > table(ExData.rma[["chip.group2"]]) > > a b c d > > 0 0 0 0 > > > > What is it that I am still doing wrong here? > > > > Best, > > Hinnerk > > > > > -----Original Message----- > > > From: bioconductor-admin@stat.math.ethz.ch > > > [mailto:bioconductor-admin@stat.math.ethz.ch] On Behalf Of > > > Wolfgang Huber > > > Sent: Thursday, January 16, 2003 10:50 AM > > > To: Hinnerk Boriss; 'Bioconductor' > > > Subject: RE: [BioC] phenodata - rtfm > > > > > > > > > Hi Hinnerk, > > > > > > It is simply a dataframe with as many rows (observations) as there are > > > columns (chips/arrays) in the exprs matrix. You can populate > > > it with data as > > > you would populate any dataframe, and use the data in models > > > and plots just > > > as with any dataframe. > > > > > > Regards > > > Wolfgang > > > > > > Division of Molecular Genome Analysis (Poustka Lab) > > > German Cancer Research Center (DKFZ) > > > Im Neuenheimer Feld 580 > > > 69120 Heidelberg, Germany > > > > > > w.huber@dkfz.de > > > http://www.dkfz.de/abt0840/whuber > > > Tel +49-6221-424709 > > > Fax +49-6221-42524709 > > > > > > > > > -----Original Message----- > > > From: bioconductor-admin@stat.math.ethz.ch > > > [mailto:bioconductor-admin@stat.math.ethz.ch]On Behalf Of > > > Hinnerk Boriss > > > Sent: Thursday, January 16, 2003 10:02 AM > > > To: 'Bioconductor' > > > Subject: [BioC] phenodata > > > > > > > > > Hi there, > > > > > > Can anyone tell me how to use the phenoData item. For one thing in a > > > technical sense of how to populate the object with data. And > > > also in the > > > analysis sense, of how to use the data once they are there. In other > > > words, is it possible use those data as factors in ANOVA or plots etc? > > > > > > Thanks for your help! > > > > > > Best, > > > Hinnerk > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor@stat.math.ethz.ch > > > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor@stat.math.ethz.ch > > > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > > > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > >
0
16.9 years ago by
Hinnerk Boriss220 wrote:
Thanks for your help! Now things work fine for me. Hinnerk > On Wed, Jan 29, 2003 at 11:31:56AM +0100, Hinnerk Boriss wrote: > > Hi there! > > I am still having difficulties setting up the phenodata properly. > > I did set up my data.frame like Wolfgang suggested to do it: > > > > chip.group <- rep(seq(1:4),each=3) > > chip.group2 <- c("a","a","a","b","b","b","c","c","c","d","d","d") > > contrasts1 <- c("T","T","T","F","F","F","T","T","T","F","F","F") > > contrasts2 <- c("F","F","F","F","F","F","T","T","T","T","T","T") > > > chip.names=c("nC1","nC2","nC3","1h1","1h2","1h3","4h1","4h2"," > 4h3","C1", > > "C2","C3") > > annotation <- > > data.frame(chip.group,chip.group2,chip.names,contrasts1,contrasts2) > > pD <- new("phenoData", pData=annotation) > > ExData@phenoData <- pD > > > > Hi, > There is a little more, > first, > class?exprSet > gets you help on the class exprSet, > in that you see that phenoData is a slot in that class that should > take a value of class phenoData, > > The documentation is found using > class?phenoData > > which says that these objects have two components, > pData and varLabels, > you only supplied one of them. > > Here is a simple example: > data(geneData) > data(geneCov) > covdesc<- list("Covariate 1", "Covariate 2", "Covariate 3") > names(covdesc) <- names(geneCov) > pdata <- new("phenoData", pData=geneCov, varLabels=covdesc) > > so you have to make up the description of the variables, as a > character vector of the right length; > > Robert > > > > > This works fine, except that the varLabels aren't set: > > > > > ExData.rma > > Expression Set (exprSet) with > > 12625 genes > > 12 samples > > phenoData object with 5 variables and 12 cases > > varLabels > > > > > > > and the covariate isn't used properly: > > table(ExData.rma[["chip.group2"]]) > > a b c d > > 0 0 0 0 > > > > What is it that I am still doing wrong here? > > > > Best, > > Hinnerk > > > > > -----Original Message----- > > > From: bioconductor-admin@stat.math.ethz.ch > > > [mailto:bioconductor-admin@stat.math.ethz.ch] On Behalf Of > > > Wolfgang Huber > > > Sent: Thursday, January 16, 2003 10:50 AM > > > To: Hinnerk Boriss; 'Bioconductor' > > > Subject: RE: [BioC] phenodata - rtfm > > > > > > > > > Hi Hinnerk, > > > > > > It is simply a dataframe with as many rows (observations) > as there are > > > columns (chips/arrays) in the exprs matrix. You can populate > > > it with data as > > > you would populate any dataframe, and use the data in models > > > and plots just > > > as with any dataframe. > > > > > > Regards > > > Wolfgang > > > > > > Division of Molecular Genome Analysis (Poustka Lab) > > > German Cancer Research Center (DKFZ) > > > Im Neuenheimer Feld 580 > > > 69120 Heidelberg, Germany > > > > > > w.huber@dkfz.de > > > http://www.dkfz.de/abt0840/whuber > > > Tel +49-6221-424709 > > > Fax +49-6221-42524709 > > > > > > > > > -----Original Message----- > > > From: bioconductor-admin@stat.math.ethz.ch > > > [mailto:bioconductor-admin@stat.math.ethz.ch]On Behalf Of > > > Hinnerk Boriss > > > Sent: Thursday, January 16, 2003 10:02 AM > > > To: 'Bioconductor' > > > Subject: [BioC] phenodata > > > > > > > > > Hi there, > > > > > > Can anyone tell me how to use the phenoData item. For one > thing in a > > > technical sense of how to populate the object with data. And > > > also in the > > > analysis sense, of how to use the data once they are > there. In other > > > words, is it possible use those data as factors in ANOVA > or plots etc? > > > > > > Thanks for your help! > > > > > > Best, > > > Hinnerk > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor@stat.math.ethz.ch > > > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor@stat.math.ethz.ch > > > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > > > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > -- > +------------------------------------------------------------- > --------------+ > | Robert Gentleman phone : (617) 632-5250 > | > | Associate Professor fax: (617) 632-2444 > | > | Department of Biostatistics office: M1B20 > | Harvard School of Public Health email: > rgentlem@jimmy.dfci.harvard.edu | > +------------------------------------------------------------- > --------------+ > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >