[BioC] no direct or inherited method for function phenoData

[James W. MacDonald]

Hi Lina,

I think you have an outdated Biobase. I have Biobase 1.10.0 and it works 
with those versions of affy and affyio.

A much better (and easier) way to install packages is to use biocLite(). 
This function will download the correct version of all requested 
packages so you shouldn't run into these problems.

source("http://www.bioconductor.org/biocLite.R")
biocLite("Biobase")

It's a pain to always type the url, so I just put the source() call in a 
file called .Rprofile in my home directory, so it is always available.

Best,

Jim

Lina Hultin-Rosenberg wrote:
> Hi Jim!
> 
> I installed the packages by using R CMD INSTALL "package name". This is the
> result of sessionInfo:
> 
> __________________________________________________________________
> 
>>sessionInfo()
> 
> Version 2.3.1 (2006-06-01)
> i686-pc-linux-gnu
> 
> attached base packages:
> [1] "tools"     "methods"   "stats"     "graphics"  "grDevices" "utils"
> [7] "datasets"  "base"
> 
> other attached packages:
>     affy   affyio  Biobase
> 1.10.0  "1.0.0"  "1.8.0"
> _____________________________________________________________________
> 
> Best regards,
> Lina
> 
> -----Ursprungligt meddelande-----
> Från: bioconductor-bounces at stat.math.ethz.ch
> [mailto:bioconductor-bounces at stat.math.ethz.ch] För James W. MacDonald
> Skickat: den 18 juli 2006 15:23
> Till: Lina Hultin-Rosenberg
> Kopia: bioconductor at stat.math.ethz.ch
> Ämne: Re: [BioC] no direct or inherited method for function phenoData
> 
> 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.
> 
> Best,
> 
> Jim
> 
> 
> 
>>_________________________________________________________________________
>>
>>
>>>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
>>
>>_______________________________________________
>>Bioconductor mailing list
>>Bioconductor at stat.math.ethz.ch
>>https://stat.ethz.ch/mailman/listinfo/bioconductor
>>Search the archives:
> 
> http://news.gmane.org/gmane.science.biology.informatics.conductor
> 
> 


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


**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.