The Create Heat Map tool simultaneously clusters samples and features, showing a two dimensional heat map of expression values. Each column corresponds to one sample, and each row corresponds to a feature (a gene or a transcript). The samples and features are both hierarchically clustered. Known metadata about each sample is added as an overlay. In addition, the following filtering and normalization are performed:
- 'log CPM' (Counts per Million) values are calculated for each gene. The CPM calculation uses the effective library sizes as calculated by the TMM normalization.
- After this, a Z-score normalization is performed across samples for each gene: the counts for each gene are mean centered, and scaled to unit variance.
- Genes or transcripts with zero expression across all samples or invalid values (NaN or +/- Infinity) are removed.
For more detail about these steps, see RNA-Seq normalization.