[BioC] Test Statistic in nbinomialTest in DESeq???
Wolfgang Huber
whuber at embl.de
Tue Sep 9 10:13:06 CEST 2014
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] <guest at bioconductor.org> 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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