[BioC] phenodata - rtfm

[Robert Gentleman]

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
> > 
> > _______________________________________________
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> > 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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