[BioC] phenodata - rtfm

[Hinnerk Boriss]

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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