[BioC] error in nbinomTest from package DESeq
whuber at embl.de
Tue Jun 29 17:57:50 CEST 2010
Thank you for the feedback!
The first thing to do here is to use a more recent version of DESeq
(last release was 1.0.4, the current devel is 1.1.5).
If that fails, the second is to make available (e.g. by using the "dump"
function in R or by posting the saved "countsTable_pi" object on a
http-server) the offending data so that we can reproduce your problem.
On Jun/21/10 6:48 PM, Andreia Fonseca wrote:
> Dear all,
> I am using DESeq package to analyze differences of expression of miRNA from
> short sequence data.
> I have a subset of sequences for which I am analyzing differences between
> treatment NS vs treatment S
> the code I am using is
> but I am getting an error message when I am making the test,
> Error: is.finite(pobs) is not TRUE
> In addition: Warning message:
> In dnbinom(x, size, prob, log) : NaNs produced
> I don't understand this, I have used this code for another subset of
> sequences and it worked just fine. Can someone tell me what I am doing
> Session Info:
> R version 2.10.1 (2009-12-14)
>  LC_COLLATE=Portuguese_Portugal.1252
> LC_CTYPE=Portuguese_Portugal.1252 LC_MONETARY=Portuguese_Portugal.1252
>  LC_NUMERIC=C LC_TIME=Portuguese_Portugal.1252
> attached base packages:
>  stats graphics grDevices datasets utils methods base
> other attached packages:
>  DESeq_0.7.12 locfit_1.5-6 lattice_0.17-26 akima_0.5-4
> loaded via a namespace (and not attached):
>  annotate_1.24.1 AnnotationDbi_1.8.2 DBI_0.2-5
> genefilter_1.28.2 geneplotter_1.24.0 grid_2.10.1
>  RColorBrewer_1.0-2 RSQLite_0.8-4 splines_2.10.1
> survival_2.35-7 xtable_1.5-6
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
More information about the Bioconductor