Hi, I can reproduce this if the simpleaffy package is loaded. If I just load the affy package, then this problem goes away. Hope this helps, Dick ********************************************************************** ********* Richard P. Beyer, Ph.D. University of Washington Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 Seattle, WA 98105-6099 http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html http://staff.washington.edu/~dbeyer ********************************************************************** ********* On Thu, 9 Nov 2006, Martin Morgan wrote: > I can't reproduce this reliably on my end, so don't really know what > is happening; does the problem persist after > >> update.packages() > > ? As a workaround, does it help to > >> library(Biobase) > > first? > > Martin > > "D.Enrique ESCOBAR ESPINOZA" <escobarebio at="" yahoo.com=""> writes: > >> can someone help me solve this mystery, >> i was using it very well but something has changed >> and it is not working any more >> can someone help me, >> the trgt file contains the abolute path to each cel.gz file in each >> line... >> ****************************** >>> print(myTarget); >> "../VESICULES.trgt" >>> print("Reading location for *CEL.gz!") ; >> "Reading location for *CEL.gz!" >>> CELlist <- scan(file=myTarget,what=list("c"),sep="\n",quiet=TRUE) ; >>> print(CELlist); >> [1] >> "/affylims/genechip/lots/VESICULES/gcos_export/R084-05MX0Z02C1.CEL.gz" >> [2] >> "/affylims/genechip/lots/VESICULES/gcos_export/R084-05MX1Z02C1.CEL.gz" >> [3] >> "/affylims/genechip/lots/VESICULES/gcos_export/R084-05MX2Z02C1.CEL.gz" >> [4] >> "/affylims/genechip/lots/VESICULES/gcos_export/R084-05MX3Z02C1.CEL.gz" >> [5] >> "/affylims/genechip/lots/VESICULES/gcos_export/R084-05MX4Z02C1.CEL.gz" >> [6] >> "/affylims/genechip/lots/VESICULES/gcos_export/R084-05MX5Z02C1.CEL.gz" >> [7] >> "/affylims/genechip/lots/VESICULES/gcos_export/R084-05MX6Z02C1.CEL.gz" >>> print("Reading location for *CEL.gz!!") ; >> "Reading location for *CEL.gz!!" >>> Data <- ReadAffy(filenames=cels) ; >> Error in function (classes, fdef, mtable) : >> unable to find an inherited method for function "pData", for >> signature "phenoData" >> Execution halted >> >> _______________________________________________ >> 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 > > -- > Martin T. Morgan > Bioconductor / Computational Biology > http://bioconductor.org >