[BioC] Why nbinomGLMTest in DESeq reports zero p values

[Wolfgang Huber]

Dear Yanzhu

one potential explanation is that the model with sex fits your data a lot better than without sex, for some genes, and that a small p-value results. Note that R (and hence DESeq) uses floating-point arithmetic, so a range of small numbers (on the real axis) are all represented by the same value (in R) of 0.

It is not unusual that expression for some genes shows a strong sex effect. For instance, if you are looking at data from a mammal, it is plausible that the X and Y chromosomes contain such genes.

	Kind regards
		Wolfgang

Il giorno 07 Feb 2014, alle ore 17:51, Yanzhu [guest] <guest at bioconductor.org> ha scritto:

> 
> I used nbinomGLMTest to compare the reduced model and full model given as below, and I got some zero for p values. Is this possible for nbinomGLMTest? If so, what's the potential reason? Thanks 
> 
> 
> Full model:
> full<-fitNbinomGLMs(cdsFull,count~Line+Rep+Sex)
> 
> Reduced model:
> reduced<-fitNbinomGLMs(cdsFull,count~Line+Rep)
> 
> 
> -- output of sessionInfo(): 
> 
> sessionInfo()
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> 
> locale:
> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C                           LC_TIME=English_United States.1252
> 
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] DESeq_1.12.1       lattice_0.20-15    locfit_1.5-9.1     Biobase_2.20.1     BiocGenerics_0.6.0 edgeR_3.2.4        limma_3.16.8
> 
> loaded via a namespace (and not attached):
> [1] annotate_1.38.0      AnnotationDbi_1.22.6 DBI_0.2-7            genefilter_1.42.0    geneplotter_1.38.0   grid_3.0.1
> [7] IRanges_1.18.4       RColorBrewer_1.0-5   RSQLite_0.11.4       splines_3.0.1        stats4_3.0.1         survival_2.37-4
> [13] XML_3.98-1.1         xtable_1.7-1
> 
> 
> 
> 
> 
> 
> --
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> 
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