Hi, I have been using the pooled-CR method of estimating dispersions with DESeq. I wish to plot the fit using the approach presented in the vignette. When I use this function with plotDispEsts(cps, "pooled") it appears to work, however when I use plotDispEsts(cds, "pooled-CR") it fails. I would appreciate advice regarding how to plot the fit for the dispersion estimation with the pooled-CR method. Please see the code below. Thank you. best wishes, Chris > plotDispEsts <- function( cds, cond ) + { + plot( + rowMeans( counts( cds, normalized=TRUE ) ), + cds@fitInfo[[cond]]$perGeneDispEsts, + pch = '.', log="xy" ) + xg <- 10^seq( -.5, 5, length.out=300 ) + lines( xg, cds@fitInfo[[cond]]$dispFun( xg ), col="red" ) + } > plotDispEsts( cds, "pooled" ) > plotDispEsts( cds, "pooled-CR" ) Error in xy.coords(x, y) : attempt to apply non-function > sessionInfo() R version 2.15.0 (2012-03-30) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] qvalue_1.30.0 DESeq_1.8.0 locfit_1.5-6 lattice_0.20-6 akima_0.5-7 Biobase_2.16.0 BiocGenerics_0.2.0 loaded via a namespace (and not attached): [1] annotate_1.34.0 AnnotationDbi_1.18.0 DBI_0.2-5 genefilter_1.38.0 geneplotter_1.34.0 grid_2.15.0 IRanges_1.14.0 MASS_7.3-17 [9] RColorBrewer_1.0-5 RSQLite_0.11.1 splines_2.15.0 stats4_2.15.0 survival_2.36-12 tcltk_2.15.0 tools_2.15.0 xtable_1.7-0 [[alternative HTML version deleted]]

Dear Chris in the parameter 'cond' of plotDispEsts you need to specify the condition for which you want to see the dispersion estimate; not the method by which it was determined. Try typing names(cds at fitInfo) to see what they are. Best wishes Wolfgang Apr/4/12 3:22 AM, chris_utah scripsit:: > Hi, > > I have been using the pooled-CR method of estimating dispersions with > DESeq. I wish to plot the fit using the approach presented in the > vignette. When I use this function with plotDispEsts(cps, "pooled") > it appears to work, however when I use plotDispEsts(cds, "pooled- CR") > it fails. I would appreciate advice regarding how to plot the fit > for the dispersion estimation with the pooled-CR method. > > Please see the code below. > > Thank you. > > best wishes, Chris > >> plotDispEsts<- function( cds, cond ) > + { + plot( + rowMeans( counts( cds, normalized=TRUE ) ), + > cds at fitInfo[[cond]]$perGeneDispEsts, + pch = '.', log="xy" ) + > xg<- 10^seq( -.5, 5, length.out=300 ) + lines( xg, > cds at fitInfo[[cond]]$dispFun( xg ), col="red" ) + } > >> plotDispEsts( cds, "pooled" ) plotDispEsts( cds, "pooled-CR" ) > Error in xy.coords(x, y) : attempt to apply non-function > >> sessionInfo() > R version 2.15.0 (2012-03-30) Platform: > x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: [1] > en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: [1] stats graphics grDevices utils > datasets methods base > > other attached packages: [1] qvalue_1.30.0 DESeq_1.8.0 > locfit_1.5-6 lattice_0.20-6 akima_0.5-7 > Biobase_2.16.0 BiocGenerics_0.2.0 > > loaded via a namespace (and not attached): [1] annotate_1.34.0 > AnnotationDbi_1.18.0 DBI_0.2-5 genefilter_1.38.0 > geneplotter_1.34.0 grid_2.15.0 IRanges_1.14.0 > MASS_7.3-17 [9] RColorBrewer_1.0-5 RSQLite_0.11.1 > splines_2.15.0 stats4_2.15.0 survival_2.36-12 > tcltk_2.15.0 tools_2.15.0 xtable_1.7-0 > > > > > [[alternative HTML version deleted]] > > _______________________________________________ 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 -- Best wishes Wolfgang Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber