DESeq problems with plotDispEst using pooled-CR
1
0
Entering edit mode
@christopher-t-gregg-4973
Last seen 9.6 years ago
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]]
• 1.3k views
ADD COMMENT
0
Entering edit mode
@wolfgang-huber-3550
Last seen 3 months ago
EMBL European Molecular Biology Laborat…
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
ADD COMMENT

Login before adding your answer.

Traffic: 706 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6