[BioC] Help please! Invalid "phenoData" object

Laurent Buffat laurent.buffat at it-omics.com
Wed Sep 17 12:14:32 MEST 2003

Hi Ying.

I have just update R (1.7.0 to 1.7.1) and also update BioConductor, and I have exacly the same error :

With the old version, your code is fine.
With the new one, it doesn't work.

I don't know how to do correctly the same goal (create phenodata) with the new version (I have just update yesterday), but I hope to have a solution soon.
So your problem is not to write code as explain in some documentation, but to know what is the change in the new version (R or bioconductor)


-----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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