[BioC] Help please! Invalid "phenoData" object

Laurent Buffat laurent.buffat at it-omics.com
Wed Sep 17 13:04:22 MEST 2003

Hi again,

just as a temporary solution, you can try this code :

(I'm suppose you have 4 chips, two factor (a and b) with 2 levels.
a <- c("a1","a1","a2","a2")
b <- c("b1","b2","b1","b2")
covar <- data.frame(a,b)
test.phe <- new("phenoData")
test.phe at pData <- covar
# or pData(test.phe) <- covar
test.phe at varLabels <- list(names(covar))
# varLabels(test.phe) <- ... doesn't work. I suppose that is the problem ...

L. Buffat

-----Message d'origine-----
De : bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch]De la part de ying chen
Envoye : mardi 16 septembre 2003 22:10
A : bioconductor at stat.math.ethz.ch
Objet : [BioC] Help please! Invalid "phenoData" object

I am new to the bioconductor and just installed the R 1.7.1 and Bioconductor
on my WinXP machine.  I followed the instruction from chris bye's A
Biologist's Guide to using Bioconductor.  Everything was fine until I
started to export the normalized data.  My test project is test.raw.  I did
load the Biobase, marrayInput, marrayNorm, marrayplot packages.  The
following is what I copied from R section:

> a <- "a"
> b <- "b"
> test.var <- cbind("a","b")
> test.phe <- new("phenoData", varLabels=test.var)
Error in validObject(.Object) : Invalid "phenoData" object: Invalid object
for slot "varLabels" in class "phenoData": got class "matrix", should be or
extend class "list"

Any suggestion?

Thanks a lot for your help,

Ying Chen

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