Hi all I'm playing around with a couple of different chromosome plots. Among others, I'm trying to use the function alongChrom from geneplotter pkg, but it seems like it hasn't really been updated from exprSet to ExpressionSet yet, although I'm using the latest version (sessionInfo below). Example: > data(ALL) > z <- buildChromLocation("hgu95av2") > alongChrom(ALL, "X", z) Error in getACExprs(eSet, usedGenes, plotFormat, scale) : no slot of name "exprs" for this object of class "ExpressionSet" In addition: Warning message: 'geneNames' is deprecated. Use 'featureNames' instead. See help("Deprecated") If I look at geneplotter:::getACExprs it seems to point back to the line that says > chromExprs <- eSet at exprs[names(usedGenes), ] instead of > chromExprs <- exprs(eSet)[names(usedGenes), ] Has the use of the alongChrom function generally been replaced by something else? Thanks \Heidi > sessionInfo() R version 2.6.0 Under development (unstable) (2007-07-17 r42258) i386-apple-darwin8.10.1 locale: en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] splines tools stats graphics grDevices utils datasets methods base other attached packages: [1] ALL_1.4.3 PFAM_1.17.0 Category_2.3.14 GO_1.17.0 [5] KEGG_1.17.0 graph_1.15.7 mouse4302_1.17.0 mouse430a2_1.17.0 [9] hgu95av2_1.17.0 genefilter_1.15.3 survival_2.32 geneplotter_1.15.1 [13] lattice_0.16-1 annotate_1.15.2 AnnotationDbi_0.0.78 RSQLite_0.6-2 [17] DBI_0.2-3 gcrma_2.9.1 matchprobes_1.9.8 limma_2.11.6 [21] affy_1.15.7 preprocessCore_0.99.7 affyio_1.5.4 Biobase_1.15.14 loaded via a namespace (and not attached): [1] KernSmooth_2.22-20 RBGL_1.13.3 RColorBrewer_1.0-1 cluster_1.11.7 grid_2.6.0

Hi Heidi, "Heidi Dvinge" <heidi at="" ebi.ac.uk=""> writes: > I'm playing around with a couple of different chromosome plots. Among > others, I'm trying to use the function alongChrom from geneplotter pkg, > but it seems like it hasn't really been updated from exprSet to > ExpressionSet yet, although I'm using the latest version (sessionInfo > below). You are correct, the code needs to be updated. Thanks for the useful report. We will have a fix available by the end of the week. Best, + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center BioC: http://bioconductor.org/ Blog: http://userprimary.net/user/