Free Online MA Plot Tool for Differential Expression Analysis

How to make an MA plot

1. Load your results. Use pre-computed results, or switch to t-test / MW mode to test raw values between two groups. You can also click Demo Data.
2. Set thresholds and the LOESS curve. Choose fold-change and p-value or FDR cutoffs, and optionally show a LOESS curve with an adjustable span.
3. Label and export. Choose how many up and down genes to label. Download PNG or SVG, export the gene list as TSV, or copy it.

Input format

Pre-computed mode needs one row per gene, with columns for ID, mean expression, log₂ fold change, and p-value. You supply mean expression yourself, such as baseMean from DESeq2 or AveExpr from limma. If it looks like raw counts, the tool offers a log₂(x+1) transform, ticked by default. Raw mode takes one column per sample, assigned to two groups. The tool then computes fold change, mean expression, and p-values with Welch's t-test, a paired t-test, or Mann-Whitney U.

How to read it

The x-axis (A) is average log₂ expression and the y-axis (M) is log₂ fold change. Most genes should sit around zero. If the LOESS curve bends away from zero, the data may have a normalization problem. Red points are up-regulated, blue points are down-regulated, and gray points miss your cutoffs.

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