[BioC] DESeq
Wolfgang Huber
whuber at embl.de
Wed May 2 22:02:13 CEST 2012
Dear Natasha
you can safely ignore the warning "In xy.coords(x, y, xlabel, ylabel,
log): 1770 y values<= 0 omitted from logarithmic plot". This is caused
by the fact that some of the dispersion estimates are zero. The plot
function is told to use a logarithmic y-axis, but is not able to deal
with the singularity of the logarithm at zero.
Maybe we can convince Simon to provide a safer and more robust version
of the plotDispEsts function in the package, which doesn't have such
warts, but in any case, the warning is not of consequence for your analysis.
Best wishes
Wolfgang
May/1/12 1:14 PM, Natasha Sahgal scripsit::
> Dear List,
>
> I am using the DESeq package to analyse some DGE data.
> At the estimate dispersion step have come across a warning message that I am unsure about.
>
> Code:
> cds<- newCountDataSet(data, conds)
> head(counts(cds))
>
> cds<- estimateSizeFactors(cds)
> sizeFactors(cds)
> cds<- estimateDispersions(cds)
> str(fitInfo(cds))
> #List of 5
> #$ perGeneDispEsts: num [1:8791] -0.05258 0.11823 0.00261 -0.00853 -0.03245 ...
> #$ dispFunc :function (q)
> # ..- attr(*, "coefficients")= Named num [1:2] 0.0152 3.0991
> # .. ..- attr(*, "names")= chr [1:2] "asymptDisp" "extraPois"
> # ..- attr(*, "fitType")= chr "parametric"
> # $ fittedDispEsts : num [1:8791] 0.2975 0.2167 0.0651 0.0619 0.1251 ...
> # $ df : int 2
> # $ sharingMode : chr "maximum"
>
> plotDispEsts(cds)
>
> Warning message:
> In xy.coords(x, y, xlabel, ylabel, log) :
> 1770 y values<= 0 omitted from logarithmic plot
>
> Do I have to change the default modes in the estimateDispersions function? Is there something I have overlooked or is it just the nature of the data?
>
> Many Thanks,
> Natasha
>
> sessionInfo()
> R version 2.15.0 (2012-03-30)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
> [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
> [7] LC_PAPER=C LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] DESeq_1.8.1 locfit_1.5-7 Biobase_2.16.0 BiocGenerics_0.2.0
> [5] WriteXLS_2.1.0 limma_3.12.0 gdata_2.8.2
>
> loaded via a namespace (and not attached):
> [1] annotate_1.34.0 AnnotationDbi_1.18.0 DBI_0.2-5
> [4] genefilter_1.38.0 geneplotter_1.34.0 grid_2.15.0
> [7] gtools_2.6.2 IRanges_1.14.2 lattice_0.20-6
> [10] RColorBrewer_1.0-5 RSQLite_0.11.1 splines_2.15.0
> [13] stats4_2.15.0 survival_2.36-12 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
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