[BioC] no direct or inherited method for function phenoData

[Lina Hultin-Rosenberg]

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:

_________________________________________________________________________
> 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
annotation=chicken
> affydata[1,1]
Error in phenoData(x) : no direct or inherited method for function
'phenoData' for this call
> affyrma<-rma(affydata)
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