[BioC] Test Statistic in nbinomialTest in DESeq???

Sarven Sabunciyan [guest] guest at bioconductor.org
Mon Sep 8 18:15:58 CEST 2014

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.



 -- output of sessionInfo(): 

> sessionInfo()
R version 3.1.0 Patched (2014-04-24 r65479)
Platform: x86_64-unknown-linux-gnu (64-bit)

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=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        

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