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


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