Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not present in R
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3 months ago
RNAseqer ▴ 260

I would like to add a dotted line threshold to a volcano plot I'm making, where my y axis represents pvalues. I would like this threshold line to be at extactly the pvalue which when FDR corrected would be an adjusted pvalue < 0.05. Some of my adjusted pvalues are less than .05 but I would like the line to fall at the exact threshold, not the largest p to make the FDR cutoff.

Is there a way to calculate this pvalue given my list of p's in R?

FDR volcano plotting R plot • 461 views
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Actually, to add an EXACT line/mark for one value based on another is impossible (for me at least). What you can do is, select the minimum p-values based on your FDR i.e., min(pvalue[FDR < 0.05]), and use it for marking.

Just out of curiosity, why don't you directly use FDR as a Y-Axis instead of a p-value?

Regards,

Nitin N.

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Well, because I want to also draw attention to nominally significant genes as they are subjected to follow up experiments and would be nice to have in the plot, and when pvalue correction is performed you get adjusted values that may be the same or nearly identcle, just due to the math of how correction is performed. With points plotted on those values they will all be overtop of one another in the y axis, rather than having the distinctive volcano shape.

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Yeah, sometimes it looks "prettier" to plot p-value rather than adjusted p-value; although either one is technically ok to plot (even multiple raw p-values can be identical).

But Nitin's suggestion is good -- I've done that before in some of my figures.

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Hmmmmm, okay.

In this case I could think of another workaround, instead of drawing line/marks, you can add another modality to your plot, Size, shape for instance, assuming you are already using different colours for differential regulation. Ex: FDR < 0.05 shape = diamond else shape = circle or something of this sort.

Regards,

Nitin N.

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