[BioC] error in nbinomTest from package DESeq

[Wolfgang Huber]

Dear Andreia

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.

	Best wishes
	Wolfgang

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
> conds_celltype<-c("NS","NS","NS","S","S","S","S","S","S")
> cds_pi_ct<-newCountDataSet(countsTable_pi,conds_celltype)
> cds_pi_ct<-estimateSizeFactors(cds_pi_ct)
> sizeFactors(cds_pi_ct)
> cds_pi_ct<-estimateVarianceFunctions(cds_pi_ct)
> res_pi_ct<-nbinomTest(cds_pi_ct,"NS","S")
> resSig_pi_ct<-res_pi_ct[res_pi_ct$padj<.1,]
> resSig_pi_ct
>
> but I am getting an error message when I am making the test,
>
> res_pi_ct<-nbinomTest(cds_pi_ct,"NS","S")
> 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
> wrong?
> Thanks
> Andreia
>
> Session Info:
>
>   sessionInfo()
> R version 2.10.1 (2009-12-14)
> i386-pc-mingw32
>
> locale:
> [1] LC_COLLATE=Portuguese_Portugal.1252
> LC_CTYPE=Portuguese_Portugal.1252    LC_MONETARY=Portuguese_Portugal.1252
> [4] LC_NUMERIC=C                         LC_TIME=Portuguese_Portugal.1252
>
>
> attached base packages:
> [1] stats     graphics  grDevices datasets  utils     methods   base
>
> other attached packages:
> [1] DESeq_0.7.12    locfit_1.5-6    lattice_0.17-26 akima_0.5-4
> Biobase_2.6.1
>
> loaded via a namespace (and not attached):
>   [1] annotate_1.24.1     AnnotationDbi_1.8.2 DBI_0.2-5
> genefilter_1.28.2   geneplotter_1.24.0  grid_2.10.1
>   [7] RColorBrewer_1.0-2  RSQLite_0.8-4       splines_2.10.1
> survival_2.35-7     xtable_1.5-6
>
>
>
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-- 


Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber