[BioC] Test Statistic in nbinomialTest in DESeq???
Sarven Sabunciyan [guest]
guest at bioconductor.org
Mon Sep 8 18:15:58 CEST 2014
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():
R version 3.1.0 Patched (2014-04-24 r65479)
Platform: x86_64-unknown-linux-gnu (64-bit)
 LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
 LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
 LC_PAPER=en_US.UTF-8 LC_NAME=C
 LC_ADDRESS=C LC_TELEPHONE=C
 LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
 parallel stats graphics grDevices datasets utils methods
other attached packages:
 DESeq_1.16.0 lattice_0.20-29 locfit_1.5-9.1
 Biobase_2.24.0 BiocGenerics_0.10.0
loaded via a namespace (and not attached):
 annotate_1.42.0 AnnotationDbi_1.26.0 DBI_0.2-7
 genefilter_1.46.1 geneplotter_1.42.0 GenomeInfoDb_1.0.2
 grid_3.1.0 IRanges_1.22.6 RColorBrewer_1.0-5
 RSQLite_0.11.4 splines_3.1.0 stats4_3.1.0
 survival_2.37-7 tools_3.1.0 XML_3.98-1.1
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