This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Why volcano plot has no points in the middle of plot?

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)?

Volcano plot

rna-seq volcano plot
• 11,000 views • link
updated by WouterDeCoster WouterDeCoster • written by rimgubaev rimgubaev

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.

• 1 views • link
written by Ram Ram

2 answers

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).

• 1 views • link
written by Benn Benn

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

• 1 views • link
written by Ram Ram

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.

• 1 views • link
written by WouterDeCoster WouterDeCoster

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

• 1 views • link
written by Benn Benn

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

• 1 views • link
written by WouterDeCoster WouterDeCoster

Log in to answer this question.

More posts like this