TimelyScholarFree Tools › Volcano Plot Generator
Make a volcano plot from DESeq2, edgeR, limma or proteomics results. Set fold-change and significance thresholds, label the top genes and download the figure and classified table.
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Using log2FoldChange as log2 fold change and pvalue as p-value (500 rows).
| Significantly up | 41log2 FC ≥ 1 and adjusted p ≤ 0.05 |
|---|---|
| Significantly down | 36log2 FC ≤ −1 |
| Not significant | 423 |
Gene, log2 fold change and p-value columns.
Fold change and (adjusted) p-value.
PNG or SVG, plus the up/down gene lists.
A volcano plot shows the size of each change (log2 fold change, x-axis) against its statistical significance (−log10 p-value, y-axis). Genes that are both strongly changed and highly significant appear in the upper left and right.
Because thousands of genes are tested, thresholds are usually applied to p-values adjusted for the false discovery rate.
Use adjusted p-values (FDR) for the cut-off; plotting raw p-values on the y-axis is common. If your table already contains adjusted values, don't adjust them again.