  Motivation: We investigate whether a template-based classification pipeline
could be used to identify immunophenotypes in (and thereby classify) a
heterogeneous disease with many subtypes. The disease we consider here is Acute
Myeloid Leukemia, which is heterogeneous at the morphologic, cytogenetic and
molecular levels, with several known subtypes. The prognosis and treatment for
AML depends on the subtype.
  Results: We apply flowMatch, an algorithmic pipeline for flow cytometry data
created in earlier work, to compute templates succinctly summarizing classes of
AML and healthy samples. We develop a scoring function that accounts for
features of the AML data such as heterogeneity to identify immunophenotypes
corresponding to various AML subtypes, including APL. All of the AML samples in
the test set are classified correctly with high confidence.
  Availability: flowMatch is available at
www.bioconductor.org/packages/devel/bioc/html/flowMatch.html; programs specific
to immunophenotyping AML are at www.cs.purdue.edu/homes/aazad/software.html.
