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Natasha
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440
@natasha-4640
Last seen 10.3 years ago
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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