Heatmaps / Expression heatmap maker
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Each row is a gene, each column a sample; colour encodes expression.
With “row z-score” on, each row is centred on its mean and divided by its standard deviation, so colours compare one gene across samples; absolute levels between genes are not comparable.
The colour range is limited to ±2 by default so a few extreme values do not wash out the rest; hover to see the raw value and the z-score.
Row clustering uses average linkage on Euclidean distances of z-scores. The order helps reveal patterns; it is not a statistical test. Heatmaps are most readable with tens to a few hundred genes, usually pre-selected differential genes.
z-scores use the sample standard deviation (n − 1); clustering uses Euclidean distance with average linkage (UPGMA), up to 400 rows.
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