title: hemaClass.org: Online One-By-One Microarray Normalization and Classification of Hematological Cancers for Precision Medicine.
abstract: BACKGROUND
  Dozens of omics based cancer classification systems have been introduced with prognostic, diagnostic, and predictive capabilities. However, they often employ complex algorithms and are only applicable on whole cohorts of patients, making them difficult to apply in a personalized clinical setting.
  
  
  RESULTS
  This prompted us to create hemaClass.org, an online web application providing an easy interface to one-by-one RMA normalization of microarrays and subsequent risk classifications of diffuse large B-cell lymphoma (DLBCL) into cell-of-origin and chemotherapeutic sensitivity classes. Classification results for one-by-one array pre-processing with and without a laboratory specific RMA reference dataset were compared to cohort based classifiers in 4 publicly available datasets. Classifications showed high agreement between one-by-one and whole cohort pre-processsed data when a laboratory specific reference set was supplied. The website is essentially the R-package hemaClass accompanied by a Shiny web application. The well-documented package can be used to run the website locally or to use the developed methods programmatically.
  
  
  CONCLUSIONS
  The website and R-package is relevant for biological and clinical lymphoma researchers using affymetrix U-133 Plus 2 arrays, as it provides reliable and swift methods for calculation of disease subclasses. The proposed one-by-one pre-processing method is relevant for all researchers using microarrays.
authors.affiliation: Department of Haematology, Aalborg University Hospital, Aalborg, Denmark.
authors.forename: Steffen
authors.initials: S
authors.lastname: Falgreen
authors.affiliation: Department of Haematology, Aalborg University Hospital, Aalborg, Denmark.|Department of Clinical Medicine, Aalborg University, Aalborg, Denmark.
authors.forename: Anders
authors.initials: A
authors.lastname: Ellern Bilgrau
authors.affiliation: Department of Haematology, Aalborg University Hospital, Aalborg, Denmark.
authors.forename: Rasmus Froberg
authors.initials: RF
authors.lastname: Brøndum
authors.affiliation: Department of Haematology, Aalborg University Hospital, Aalborg, Denmark.|Department of Clinical Medicine, Aalborg University, Aalborg, Denmark.
authors.forename: Lasse
authors.initials: L
authors.lastname: Hjort Jakobsen
authors.affiliation: Department of Haematology, Aalborg University Hospital, Aalborg, Denmark.|Department of Clinical Medicine, Aalborg University, Aalborg, Denmark.
authors.forename: Jonas
authors.initials: J
authors.lastname: Have
authors.affiliation: Department of Haematology, Aalborg University Hospital, Aalborg, Denmark.|Department of Clinical Medicine, Aalborg University, Aalborg, Denmark.
authors.forename: Kasper
authors.initials: K
authors.lastname: Lindblad Nielsen
authors.affiliation: Department of Haematology, Aalborg University Hospital, Aalborg, Denmark.|Department of Clinical Medicine, Aalborg University, Aalborg, Denmark.
authors.forename: Tarec Christoffer
authors.initials: TC
authors.lastname: El-Galaly
authors.affiliation: Department of Haematology, Aalborg University Hospital, Aalborg, Denmark.
authors.forename: Julie Støve
authors.initials: JS
authors.lastname: Bødker
authors.affiliation: Department of Haematology, Aalborg University Hospital, Aalborg, Denmark.
authors.forename: Alexander
authors.initials: A
authors.lastname: Schmitz
authors.affiliation: Department of Hematopathology, University of Texas MD Anderson Cancer Center, Houston, United States of America.
authors.forename: Ken
authors.initials: K
authors.lastname: H Young
authors.affiliation: Department of Haematology, Aalborg University Hospital, Aalborg, Denmark.|Department of Clinical Medicine, Aalborg University, Aalborg, Denmark.
authors.forename: Hans Erik
authors.initials: HE
authors.lastname: Johnsen
authors.affiliation: Department of Haematology, Aalborg University Hospital, Aalborg, Denmark.|Department of Clinical Medicine, Aalborg University, Aalborg, Denmark.
authors.forename: Karen
authors.initials: K
authors.lastname: Dybkær
authors.affiliation: Department of Haematology, Aalborg University Hospital, Aalborg, Denmark.|Department of Clinical Medicine, Aalborg University, Aalborg, Denmark.
authors.forename: Martin
authors.initials: M
authors.lastname: Bøgsted
mesh_terms: D000328:Adult; D000368:Aged; D019295:Computational Biology / Q000379:methods; D066264:Datasets as Topic; D020869:Gene Expression Profiling; D019337:Hematologic Neoplasms / Q000175:diagnosis* / Q000188:drug therapy / Q000235:genetics*; D006801:Humans; D008297:Male; D008875:Middle Aged; D000072638:Patient Portals; D057285:Precision Medicine / Q000379:methods; D015203:Reproducibility of Results; D012984:Software; D064878:Web Browser; D057188:Workflow