[BioC] DESeq problems with plotDispEst using pooled-CR

[Wolfgang Huber]

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]]
>
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-- 
Best wishes
	Wolfgang

Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber