Question: phenodata  rtfm
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rgentleman • 5.5k 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: bioconductoradmin@stat.math.ethz.ch
> > [mailto:bioconductoradmin@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 +496221424709
> > Fax +49622142524709
> >
> >
> > Original Message
> > From: bioconductoradmin@stat.math.ethz.ch
> > [mailto:bioconductoradmin@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
> >
>
> _______________________________________________
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 Robert Gentleman phone : (617) 6325250

 Associate Professor fax: (617) 6322444

 Department of Biostatistics office: M1B20
 Harvard School of Public Health email:
rgentlem@jimmy.dfci.harvard.edu 
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modified 16.9 years ago
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Hinnerk Boriss • 220
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16.9 years ago by
rgentleman • 5.5k