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How do I visualise an expression matrix?

Make a heatmap

Clustered heatmaps, and the scaling decision that changes what they show.

Nearly every decision here is about scaling. Row-scaling (z-scores per gene) shows relative patterns across conditions and discards absolute abundance; unscaled data shows abundance and lets highly expressed genes dominate the colour range. Both are legitimate and they answer different questions, so state which you used.

Clustering rows groups genes with similar behaviour. Clustering columns is a check on your experiment: if replicates do not cluster together, that is worth knowing before the figure.

A red–green colour scale is unreadable to roughly 8% of men. Use a perceptually uniform diverging scale such as blue–white–red instead.

What to use

If you script

Command-line and library options. No page here — they need an environment rather than a browser.

Drafted from the literature and not yet reviewed by a specialist. Treat it as a starting point, and tell us if something here is wrong. Last touched .

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