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   




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