[BioC] DESeq

[Wolfgang Huber]

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