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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 m?thode directe ou h?rit?e 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 "1.6.4" "1.5.15" "1.10.1" That is an outdated version of affy, so you should re-install that as well.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]] > > > > -------------------------------------------------------------------- ---- > > _______________________________________________ > 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.