[BioC] no direct or inherited method for function phenoData

James W. MacDonald jmacdon at med.umich.edu
Tue Jul 18 15:23:05 CEST 2006

Hi Lina,

Lina Hultin-Rosenberg wrote:
> Hi!
> I am a beginner at using R and bioconductor packages so this question might
> have an easy answer, although not obvious to me after searching the web. I
> am analyzing some affymetrix data using affy and other packages. When I
> started everything was working fine and I was using rma() and gcrma() to
> pre-process the data but then the problem started. I seem to have problems
> with the phenodata slot, I get an error message involving phenodata for
> almost anything I try out. Some examples below:

This looks like you have incompatible versions of Biobase and affy. How 
exactly did you install the packages? Also, please send the results of 
sessionInfo() after you have loaded the affy package.



> _________________________________________________________________________
> Loading required package: Biobase
> Loading required package: tools
> Welcome to Bioconductor
>         Vignettes contain introductory material.
>         To view, simply type 'openVignette()' or start with 'help(Biobase)'.
>         For details on reading vignettes, see the openVignette help page.
> Loading required package: affyio
> AffyBatch object
> size of arrays=984x984 features (181558 kb)
> cdf=Chicken (38535 affyids)
> number of samples=24
> number of genes=38535
> annotation=chicken
> Error in phenoData(x) : no direct or inherited method for function
> 'phenoData' for this call
> Background correcting
> Normalizing
> Calculating Expression
> Error in phenoData(object) : no direct or inherited method for function
> 'phenoData' for this call
> ________________________________________________________________________
> I have tried the same on the affybatch.example data and gets the same error
> message. I have repeated the steps many times, re-installed R and packages
> and read the raw data from the CD again to make sure everything is ok but I
> still get the same problems.
> I would really appreciate if I could get some help in this matter! As it is
> now, I can't do any analysis at all since everything I try gets interrupted
> by this error message.
> Thank you!
> Best regards,
> Lina Hultin Rosenberg   
> ________________________________
> Lina Hultin Rosenberg
> Msc Molecular Biotechnology
> Evolutionary Biology Department
> Uppsala University
> Norbyvägen 18
> 752 36 Uppsala
> Phone: +46-18-4716444
> Email: lina.hultin.rosenberg at ebc.uu.se
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James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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