One-sided p-value from DESeq2
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@tkuilman-6868
Last seen 6 months ago
Netherlands

For downstream analysis using a modified version of Robust Rank Aggregation (alpha-RRA; Li, et al. Genome Biology 2014), I would like to obtain one-tailed p-values from a standard DESeq2 analysis using a Wald test (rather than the two-tailed p-values that are represented in a 'DESeqResults' object). Can this be done from a 'DESeqDataSet' or a 'DESeqResults' object using DESeq2, and if so what steps should I take to do that?

Thanks, Thomas

DESeq2 nbinomWaldTest one-sided p-value • 1.4k views
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@mikelove
Last seen 18 hours ago
United States

See the vignette section on threshold tests. You would set lfcThreshold to 0 and specify the alternative as less than or greater than.

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Fantastic, that's right what I need. Thanks for your quick reply; I should have spotted the altHypothesis argument of the results() function but apparently read past that.