[BioC] phenodata - rtfm
Hinnerk Boriss
boriss@izbi.uni-leipzig.de
Wed, 29 Jan 2003 15:38:17 +0100
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
> > >
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> >
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>
> --
> +-------------------------------------------------------------
> --------------+
> | 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 |
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