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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 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