The Create Heat Map for Abundance Table tool simultaneously clusters samples and features (taxa), showing a two dimensional heat map of taxonomic abundances.
The following filtering and normalization is performed:
- 'log CPM' (Counts per Million) values are calculated for each feature. The CPM calculation uses the effective library sizes as calculated by the TMM normalization.
- Z-score normalization is performed across samples for each feature: the counts for each feature are mean centered, and scaled to unit variance.
For more detail about these steps, see http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=RNA_Seq_normalization.html.