Re: Test Statistic in nbinomialTest in DESeq???

Dear Sarven

depending on how one wants to view it, the test statistic is either:
- (a) bivariate and given by the pair of observed count sums (kiA, kiB),
- (b) that p-value, itself.
The spirit of the journal guidelines would probably best satisfied by stating either (a) or the ratio kiA/kiB.

Best wishes	
	Wolfgang


Il giorno 08 Sep 2014, alle ore 18:15, Sarven Sabunciyan [guest] <[email protected]> ha scritto:

> Hi everyone,
> 
> Does nbinomialTest in DESeq calculate a test statistic? According to DESeq documentation, "nbinomTest calculates a p value by summing up the probabilities of all per-group count sums a and b that sum up to the observed count sum kiS and are more extreme than the observed count sums kiA and kiB. "
> 
> The journal we are submitting our work to requires that we state both the test statistic and the p-value in our results. Since our analysis was performed using DESeq, I need to know how to extract the test statistic or make a statement about how the p-value is calculated. Any help/advice on this matter would be greatly appreciated.
> 
> Thanks
> 
> Sarven 
> 
> -- output of sessionInfo(): 
> 
>> sessionInfo()
> R version 3.1.0 Patched (2014-04-24 r65479)
> Platform: x86_64-unknown-linux-gnu (64-bit)
> 
> locale:
> [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
> [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
> [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
> [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
> [9] LC_ADDRESS=C               LC_TELEPHONE=C            
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
> 
> attached base packages:
> [1] parallel  stats     graphics  grDevices datasets  utils     methods  
> [8] base     
> 
> other attached packages:
> [1] DESeq_1.16.0        lattice_0.20-29     locfit_1.5-9.1     
> [4] Biobase_2.24.0      BiocGenerics_0.10.0
> 
> loaded via a namespace (and not attached):
> [1] annotate_1.42.0      AnnotationDbi_1.26.0 DBI_0.2-7           
> [4] genefilter_1.46.1    geneplotter_1.42.0   GenomeInfoDb_1.0.2  
> [7] grid_3.1.0           IRanges_1.22.6       RColorBrewer_1.0-5  
> [10] RSQLite_0.11.4       splines_3.1.0        stats4_3.1.0        
> [13] survival_2.37-7      tools_3.1.0          XML_3.98-1.1        
> [16] xtable_1.7-3        
> 
> --
> Sent via the guest posting facility at bioconductor.org.
> 
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