[BioC] phenodata - rtfm

[Hinnerk Boriss]

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

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
>