title: TMA-Combiner, a simple software tool to permit analysis of replicate cores on tissue microarrays.
abstract: We have previously published a suite of software tools that facilitates the reformulation of tissue microarray (TMA) data so that it may be analyzed using techniques originally devised for analysis of cDNA microarray data. However, current microarray data often feature multiple scores for a given tissue sample and antibody combination. Furthermore, an efficient and systematic method for combining scores that takes into account the differing staining properties of tissue epitopes has not been described. We thus present the TMA-Combiner, a new Microsoft Excel-based macro that permits analysis of data for which tissues may have two or more scores per antibody, and permits combination of data from multiple different tissue microarrays. It accomplishes this by rendering one score per tissue per antibody from two or more scores, using one of multiple user-selectable combination rules developed to account for the differing staining properties of tissue epitopes. This greatly facilitates analysis of tissue microarrays, particularly for users with large repositories of data, and may facilitate discovery of biological trends and help refine diagnostic accuracy of tissue markers in clinical samples.
authors.affiliation: Biological and Biomedical Sciences Program, Division of Medical Sciences, Harvard Medical School, Cambridge, MA 02138, USA. clliu@fas.harvard.edu
authors.forename: Chih Long
authors.initials: CL
authors.lastname: Liu
authors.forename: Kelli D
authors.initials: KD
authors.lastname: Montgomery
authors.forename: Yasodha
authors.initials: Y
authors.lastname: Natkunam
authors.forename: Robert B
authors.initials: RB
authors.lastname: West
authors.forename: Torsten O
authors.initials: TO
authors.lastname: Nielsen
authors.forename: Maggie C U
authors.initials: MC
authors.lastname: Cheang
authors.forename: Dmitry A
authors.initials: DA
authors.lastname: Turbin
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Marinelli
authors.forename: Matt
authors.initials: M
authors.lastname: van de Rijn
authors.forename: John P T
authors.initials: JP
authors.lastname: Higgins
mesh_terms: D016000:Cluster Analysis; D006801:Humans; D008490:Medical Informatics / Q000295:instrumentation* / Q000379:methods*; D009363:Neoplasm Proteins / Q000145:classification / Q000378:metabolism; D009369:Neoplasms / Q000145:classification / Q000175:diagnosis / Q000378:metabolism; D015203:Reproducibility of Results; D012984:Software; D046888:Tissue Array Analysis / Q000295:instrumentation* / Q000379:methods
chemical_list: D009363:Neoplasm Proteins