FDR = 0 ?

[Andre Gerber]

Dear Team

I have a question regarding the FDRs or p-value resulting from ORA or GSEA analysis of gene sets – I am not clear about the threshold for indication of an FDR = 0 in the table?

For example, If a GO term is highly overrepresented/enriched, the table indicates this with FDR = 0. As an FDR = 0 is not possible, I assume you have a certain threshold for indicating a FDR = 0 (same for p-value = 0). For example, you may have set that everything smaller than 10E-10 appears as FDR = 0?

 We aim to publish data from your analysis and I should whether or how to explain an FDR = 0 to a referee?

 Thanks much!

Kind regards,

Andre Gerber

[Yuxing Liao]

Hi Andre,

FDR zero just means it is smaller than 2.2e-16. See double.eps  in https://stat.ethz.ch/R-manual/R-devel/library/base/html/zMachine.html

Yuxing

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