[BioC] Error in validityMethod(object): No slot of name"phenoLabels" for this object o

[James MacDonald]

Suresh,

You should not cross-post questions to both BioC and R-help. This is
considered bad form, and will not increase your chances of getting a
helpful response (but will increase your chances of getting an abrupt
rejoinder). This is clearly a BioC question.

I haven't seen this particular error, so I am not sure of the exact
cause. However, it appears that the BioC core are adding some new S4
objects to Bioconductor, and your version of affy is somehow out of
synch with another required package (probably Biobase). 

I checked the current version of affy devel, and it is still out of
synch with Biobase because there is a new object called an exprMatrix in
Biobase that hasn't made it to the current devel version of affy. Any
new AffyBatch will fail because the se.exprs and exprs slots are
supposed to be class exprMatrix but are class matrix instead.

All this aside, there are two things you can do. First, update your
bioconductor packages to the newest devel version and then download and
build the affy tarball from the cvs page. If you don't know how to do
this, then you can simply wait a day or two for the new affy build to
appear on bioconductor. Probably affy 1.3.26 is what you will need.

HTH,

Jim



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623

>>> "Suresh Kumar Karanam" <sureshkaran at hotmail.com> 10/27/03 05:33PM
>>>
Hi,
I was using the affy package in R for sometime. I reinstalled the R  
environment lately due to some other issues and now I get errors when I
use 
the function ReadAffy. The error is reproduced here:

Error in validityMethod(object): No slot of name "phenoLabels" for this

object of class "phenoData"

I don't know what's wrong. Any help appreciated.
thanks,
suresh

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