I am using DESeq package for RNAseq analyses and I am getting the following errir with plotPCA fucntion: print(plotPCA(vsd, intgroup=c("condition"))) Error in print(plotPCA(vsd, intgroup = c("condition"))) : error in evaluating the argument 'x' in selecting a method for function 'print': Error: could not find function "plotPCA" -- output of sessionInfo(): > sessionInfo() R version 2.15.1 (2012-06-22) Platform: x86_64-redhat-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] grid stats graphics grDevices utils datasets methods base other attached packages: [1] DESeq_1.8.3 limma_3.12.3 VennDiagram_1.5.1 RColorBrewer_1.0-5 [5] pcaMethods_1.42.0 Rcpp_0.9.14 pls_2.3-0 BiocInstaller_1.4.7 [9] gplots_2.11.0 MASS_7.3-20 KernSmooth_2.23-8 caTools_1.13 [13] bitops_1.0-4.1 gdata_2.12.0 gtools_2.7.0 locfit_1.5-8 [17] Biobase_2.16.0 BiocGenerics_0.2.0 loaded via a namespace (and not attached): [1] annotate_1.34.1 AnnotationDbi_1.18.1 DBI_0.2-5 genefilter_1.38.0 [5] geneplotter_1.34.0 IRanges_1.14.4 lattice_0.20-6 RSQLite_0.11.1 [9] splines_2.15.1 stats4_2.15.1 survival_2.36-14 tools_2.15.1 [13] XML_3.9-4 xtable_1.7-0 -- Sent via the guest posting facility at bioconductor.org.

Dear Janake The function plotPCA is a recent addition to DESeq. Please update to the latest (release) version of the package, see http://www.bioconductor.org/packages/release/bioc/html/DESeq.html Note that the documentation of the package comes with it. Making sure that the documentation that you are consulting matches the software that you have installed should avoid such confusion in the future. Enjoy, Wolfgang Il giorno Oct 4, 2012, alle ore 3:33 PM, Janake Wije [guest] <guest at="" bioconductor.org=""> ha scritto: > > > I am using DESeq package for RNAseq analyses and I am getting the following errir with plotPCA fucntion: > > print(plotPCA(vsd, intgroup=c("condition"))) > Error in print(plotPCA(vsd, intgroup = c("condition"))) : > error in evaluating the argument 'x' in selecting a method for > function 'print': Error: could not find function "plotPCA" > > > > -- output of sessionInfo(): > >> sessionInfo() > R version 2.15.1 (2012-06-22) > Platform: x86_64-redhat-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 > [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C > [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] grid stats graphics grDevices utils datasets methods base > > other attached packages: > [1] DESeq_1.8.3 limma_3.12.3 VennDiagram_1.5.1 RColorBrewer_1.0-5 > [5] pcaMethods_1.42.0 Rcpp_0.9.14 pls_2.3-0 BiocInstaller_1.4.7 > [9] gplots_2.11.0 MASS_7.3-20 KernSmooth_2.23-8 caTools_1.13 > [13] bitops_1.0-4.1 gdata_2.12.0 gtools_2.7.0 locfit_1.5-8 > [17] Biobase_2.16.0 BiocGenerics_0.2.0 > > loaded via a namespace (and not attached): > [1] annotate_1.34.1 AnnotationDbi_1.18.1 DBI_0.2-5 genefilter_1.38.0 > [5] geneplotter_1.34.0 IRanges_1.14.4 lattice_0.20-6 RSQLite_0.11.1 > [9] splines_2.15.1 stats4_2.15.1 survival_2.36-14 tools_2.15.1 > [13] XML_3.9-4 xtable_1.7-0 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor