[BioC] no direct or inherited method for function phenoData

Lina Hultin-Rosenberg Lina.Hultin.Rosenberg at ebc.uu.se
Tue Jul 18 14:39:54 CEST 2006


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:

> library(affy)
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
> affydata<-ReadAffy()
> affydata
AffyBatch object
size of arrays=984x984 features (181558 kb)
cdf=Chicken (38535 affyids)
number of samples=24
number of genes=38535
> affydata[1,1]
Error in phenoData(x) : no direct or inherited method for function
'phenoData' for this call
> affyrma<-rma(affydata)
Background correcting
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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