Why volcano plot has no points in the middle of plot?

Question

[rimgubaev]

Here is an example of volcano plot produced using edgeR results on DEG analysis. So my question is why there is no values in the middle of plot (indicated by red circle)?

[Ram]

Plots depict data graphically. When a plot does not depict a point at a co-ordinate, it usually means that there was no matching data point. In your case, there was no gene with with a low fold change at the Q values covered by the blank region.

Answer 1

[Benn]

This is because there is a relationship between p-value and fold change. With no fold change (log2FC = 0) you have no significant difference hence p-value of 1 which is zero after -10log. With higher FC you can get lower p-values (hence higher -log10 values).

[Ram]

Do you mean q values, perhaps? That's on the plot, not p-values.

[Benn]

I assume q-value is used for FDR adjusted p-value in this case.

Answer 2

[WouterDeCoster]

You are plotting the fold change of differential expression versus the confidence in detecting this differential expression. (q-value) Genes which have a low fold change will generally have a higher q-score.

[Benn]

Lower fold change will result generally in higher q-values (p-values). Higher means less significant...

[WouterDeCoster]

Oh yeah, exactly :)
[thanks for noticing - adapted]