DiffBind t-statistic values
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@lindsaynhayes-13285
Last seen 9 weeks ago
United States

In the DiffBind package, how can I extract the t-statistic from the dba.report?

r DiffBind ATAC • 117 views
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Rory Stark ★ 4.1k
@rory-stark-5741
Last seen 17 days ago
CRUK, Cambridge, UK

DiffBind does not use t-statistics to determine the confidence in assessing differential binding. T-tests assume that the read counts can be accurately modelled using a normal distribution, which is an invalid assumption for these data. Instead we use an FDR-corrected p-value computed using exact tests from the DESeq2 and/or edgeR packages.

These confidence statistics can be retrieved as the $FDR values in the report returned by dba.report(): data(tamoxifen_analysis) report <- dba.report(tamoxifen, th=.01) report$FDR