[BioC] problem in gcrma with phenoData

[James W. MacDonald]

Hi Florence,

Florence Combes wrote:
> Dear all,
> 
> More than a year ago, I ran affymetrix analysis with gcrma without problem.
> I redo now the same command but apparently I have a problem with phenoData()
> :
> 
> -------------------------------------
> raw.data <- ReadAffy()
> 
>>eset <- gcrma(raw.data)
> 
> Adjusting for optical effect..........Done.
> Computing affinities.Done.
> Adjusting for non-specific binding..........Done.
> Normalizing
> Calculating Expression
> Erreur dans phenoData(object) : pas de méthode directe ou héritée pour la
> fonction 'phenoData' dans cet appel
> -------------------------------------
> 
> I saw on the list that it could be due to changes in the Biobase package
> which is now more "stringent" about the structure of the data ; I have 10
> CEL files from hybridizations on hgu133plus2 arrays.
> 
> some more info :
> 
> 
>>sessionInfo()
> 
> Version 2.3.1 (2006-06-01)
> i486-pc-linux-gnu
> 
> attached base packages:
> [1] "splines"   "tools"     "methods"   "stats"     "graphics"  "grDevices"
> [7] "utils"     "datasets"  "base"
> 
> other attached packages:
> hgu133plus2probe   hgu133plus2cdf            gcrma      matchprobes
>            "1.0"          "1.4.3"          "2.4.1"          "1.4.0"
>             affy       reposTools          Biobase
>          "1.6.4"         "1.5.15"         "1.10.1"

That is an outdated version of affy, so you should re-install that as 
well. Make sure that you get affyio when affy is installed (it is a 
dependency, and should be installed if you use biocLite).

You might just try biocLite() without arguments to make sure most of 
your packages are updated. It appears that you have a mixture of new and 
old packages that are causing conflicts.

HTH,

Jim


> 
> _______________
> 
> Thank you very much for your help,
> 
> Florence.
> 
> 	[[alternative HTML version deleted]]
> 
> 
> 
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-- 
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


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