
Hi Jim,
 
I updated R and re-installed BioC into the same folder as previous versions in order to keep the libraries.  You are right about it.  This causes the problem.  After deleting all the files, I re-installed R and BioC again, and everyting works beautifully.
 
Thanks a lot, I really appreciate it.
 
Jason
 
 
> Date: Thu, 10 Jan 2008 15:29:59 -0500> From: jmacdon@med.umich.edu> To: pridelands88@hotmail.com> CC: bioconductor@stat.math.ethz.ch> Subject: Re: [BioC] plotHist and plotDeg error> > How exactly did you re-install BioC? I ask because you have a mixture of > BioC2.0 and BioC2.1, which is likely causing at least some of the problems.> > Also, what exactly is celData?> > Best,> > Jim> > > > Jason Pear wrote:> > Hi Dear BioC,> > > > The plotHist and plotDeg worked well before, however, they gave me some error messages today. I reinstall the R-2.6.1 and BioConductor and the errors stay the same.> > > > Any suggestions?> > > > Many thanks,> > > > Jason> > > > # ----------------------> >> plotDeg(celData)> > Error in UseMethod("as.double") : no applicable method for "as.double"> > In addition: Warning message:> > ':::' is deprecated.> > 'methods' is deprecated.> > 'seemsS4Object' is deprecated.> > Use 'isS4' instead.> > See help("Deprecated") > > > >> plotHist(celData)> > Error in checkSlotAssignment(object, name, value) : > > ".Data" is not a slot in class "matrix"> > In addition: Warning message:> > In par(op) : calling par(new=) with no plot> > > >> sessionInfo()> > R version 2.6.1 (2007-11-26) > > i386-pc-mingw32 > > locale:> > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252> > attached base packages:> > [1] splines tools stats graphics grDevices utils datasets methods base > > other attached packages:> > [1] hgu133plus2cdf_1.16.0 affycoretools_1.10.2 annaffy_1.10.1 gcrma_2.10.0 > > [5] matchprobes_1.10.0 biomaRt_1.10.1 RCurl_0.8-0 XML_1.7-1 > > [9] GOstats_2.2.6 Category_2.2.3 Matrix_0.99875-1 lattice_0.17-2 > > [13] genefilter_1.16.0 survival_2.34 KEGG_1.16.1 RBGL_1.12.0 > > [17] annotate_1.16.1 xtable_1.5-2 AnnotationDbi_1.0.6 RSQLite_0.6-4 > > [21] DBI_0.2-4 GO_1.16.0 graph_1.14.2 limma_2.12.0 > > [25] affy_1.16.0 preprocessCore_1.0.0 affyio_1.6.1 Biobase_1.16.1 > > loaded via a namespace (and not attached):> > [1] cluster_1.11.9 grid_2.6.1 > > > > _________________________________________________________________> > > > > > GLM_CPC_VideoChat_distantfamily_012008> > [[alternative HTML version deleted]]> > > > _______________________________________________> > Bioconductor mailing list> > Bioconductor@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
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