Question: One-sided p-value from DESeq2
0
gravatar for t.kuilman
4 months ago by
t.kuilman140
Netherlands
t.kuilman140 wrote:

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

ADD COMMENTlink modified 4 months ago by Michael Love21k • written 4 months ago by t.kuilman140
Answer: One-sided p-value from DESeq2
2
gravatar for Michael Love
4 months ago by
Michael Love21k
United States
Michael Love21k wrote:

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

ADD COMMENTlink written 4 months ago by Michael Love21k

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.

ADD REPLYlink written 4 months ago by t.kuilman140
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