Critical assessment of automated flow cytometry data analysis techniques
Nima Aghaeepour,Greg Finak,Holger H. Hoos,Tim R. Mosmann,Ryan R. Brinkman,Raphael Gottardo,Richard H. Scheuermann +6 more
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Several methods performed well as compared to manual gating or external variables using statistical performance measures, which suggests that automated methods have reached a sufficient level of maturity and accuracy for reliable use in FCM data analysis.Abstract:
Traditional methods for flow cytometry (FCM) data processing rely on subjective manual gating. Recently, several groups have developed computational methods for identifying cell populations in multidimensional FCM data. The Flow Cytometry: Critical Assessment of Population Identification Methods (FlowCAP) challenges were established to compare the performance of these methods on two tasks: (i) mammalian cell population identification, to determine whether automated algorithms can reproduce expert manual gating and (ii) sample classification, to determine whether analysis pipelines can identify characteristics that correlate with external variables (such as clinical outcome). This analysis presents the results of the first FlowCAP challenges. Several methods performed well as compared to manual gating or external variables using statistical performance measures, which suggests that automated methods have reached a sufficient level of maturity and accuracy for reliable use in FCM data analysis.read more
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Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis.
Jacob H. Levine,Erin F. Simonds,Sean C. Bendall,Kara L. Davis,El-ad David Amir,Michelle D. Tadmor,Oren Litvin,Harris G. Fienberg,Astraea Jager,Eli R. Zunder,Rachel Finck,Amanda Larson Gedman,Ina Radtke,James R. Downing,Dana Pe'er,Garry P. Nolan +15 more
TL;DR: Using hematopoietic progenitors, a signaling-based measure of cellular phenotype was defined, which led to isolation of a gene expression signature that was predictive of survival in independent cohorts, yielding insights into AML pathophysiology.
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Mass Cytometry: Single Cells, Many Features.
TL;DR: The current state of mass cytometry is reviewed, providing an overview of the instrumentation, its present capabilities, and methods of data analysis, as well as thoughts on future developments and applications.
Journal ArticleDOI
Guidelines for the use of flow cytometry and cell sorting in immunological studies (second edition)
Andrea Cossarizza,Hyun-Dong Chang,Andreas Radbruch,Andreas Acs,Dieter Adam,Sabine Adam-Klages,William W. Agace,William W. Agace,Nima Aghaeepour,Mübeccel Akdis,Matthieu Allez,Larissa Nogueira Almeida,Giorgia Alvisi,Graham Anderson,Immanuel Andrä,Francesco Annunziato,Achille Anselmo,Petra Bacher,Cosima T. Baldari,Sudipto Bari,Vincenzo Barnaba,Vincenzo Barnaba,Joana Barros-Martins,Luca Battistini,Wolfgang Bauer,Sabine Baumgart,Nicole Baumgarth,Dirk Baumjohann,Bianka Baying,Mary Bebawy,Burkhard Becher,Wolfgang Beisker,Vladimir Benes,Rudi Beyaert,Alfonso Blanco,Dominic A. Boardman,Christian Bogdan,Jessica G. Borger,Giovanna Borsellino,Philip E. Boulais,Jolene Bradford,Dirk Brenner,Dirk Brenner,Ryan R. Brinkman,Anna E. S. Brooks,Dirk H. Busch,Martin Büscher,Timothy P. Bushnell,Federica Calzetti,Garth Cameron,Ilenia Cammarata,Xuetao Cao,Susanna Cardell,Stefano Casola,Marco A. Cassatella,Andrea Cavani,Antonio Celada,Lucienne Chatenoud,Pratip K. 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Oja,Diana Ordonez,Alberto Orfao,Eva Orlowski-Oliver,Wenjun Ouyang,Annette Oxenius,Raghavendra Palankar,Isabel Panse,Kovit Pattanapanyasat,Malte Paulsen,Dinko Pavlinic,Livius Penter,Pärt Peterson,Christian Peth,Jordi Petriz,Federica Piancone,Winfried F. Pickl,Silvia Piconese,Marcello Pinti,A. Graham Pockley,Malgorzata J. Podolska,Zhiyong Poon,Katharina Pracht,Immo Prinz,Carlo Pucillo,Sally A. Quataert,Linda Quatrini,Kylie M. Quinn,Kylie M. Quinn,Helena Radbruch,Tim R. Radstake,Susann Rahmig,Hans-Peter Rahn,Bartek Rajwa,Gevitha Ravichandran,Yotam Raz,Jonathan Rebhahn,Diether J. Recktenwald,Dorothea Reimer,Caetano Reis e Sousa,Ester B. M. Remmerswaal,Lisa Richter,Laura G. Rico,Andy Riddell,Aja M. Rieger,J. 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Stall,Natalie Stanley,Regina Stark,Christina Stehle,Tobit Steinmetz,Hannes Stockinger,Yousuke Takahama,Kiyoshi Takeda,Leonard Tan,Leonard Tan,Attila Tárnok,Attila Tárnok,Attila Tárnok,Gisa Tiegs,Gergely Toldi,Julia Tornack,Elisabetta Traggiai,Mohamed Trebak,Timothy Tree,Timothy Tree,Joe Trotter,John Trowsdale,Maria Tsoumakidou,Henning Ulrich,Sophia Urbanczyk,Willem van de Veen,Maries van den Broek,Edwin van der Pol,Sofie Van Gassen,Gert Van Isterdael,René A. W. van Lier,Marc Veldhoen,Salvador Vento-Asturias,Paulo Vieira,David Voehringer,Hans-Dieter Volk,Anouk von Borstel,Konrad von Volkmann,Ari Waisman,Rachael C. Walker,Paul K. Wallace,Sa A. Wang,Xin M. Wang,Michael D. Ward,Kirsten A. Ward-Hartstonge,Klaus Warnatz,Gary Warnes,Sarah Warth,Claudia Waskow,Claudia Waskow,James V. Watson,Carsten Watzl,Leonie Wegener,Thomas Weisenburger,Annika Wiedemann,Jürgen Wienands,Anneke Wilharm,Robert J. Wilkinson,Robert J. Wilkinson,Robert J. Wilkinson,Gerald Willimsky,James B. Wing,Rieke Winkelmann,Thomas Winkler,Oliver F. Wirz,Alicia Wong,Peter Wurst,Jennie H M Yang,Jennie H M Yang,Juhao Yang,Maria Yazdanbakhsh,Liping Yu,Alice Yue,Hanlin Zhang,Yi Zhao,Susanne Ziegler,Christina E. Zielinski,Jakob Zimmermann,Arturo Zychlinsky +462 more
TL;DR: These guidelines are a consensus work of a considerable number of members of the immunology and flow cytometry community providing the theory and key practical aspects offlow cytometry enabling immunologists to avoid the common errors that often undermine immunological data.
Journal ArticleDOI
Guidelines for the use of flow cytometry and cell sorting in immunological studies
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TL;DR: A rapid search in PubMed shows that using "flow cytometry immunology" as a search term yields more than 68 000 articles, the first of which is not about lymphocytes as mentioned in this paper.
References
More filters
Journal ArticleDOI
The WEKA data mining software: an update
TL;DR: This paper provides an introduction to the WEKA workbench, reviews the history of the project, and, in light of the recent 3.6 stable release, briefly discusses what has been added since the last stable version (Weka 3.4) released in 2003.
Book
An Introduction to Support Vector Machines and Other Kernel-based Learning Methods
TL;DR: This is the first comprehensive introduction to Support Vector Machines (SVMs), a new generation learning system based on recent advances in statistical learning theory, and will guide practitioners to updated literature, new applications, and on-line software.
Book
Finding Groups in Data: An Introduction to Cluster Analysis
TL;DR: An electrical signal transmission system, applicable to the transmission of signals from trackside hot box detector equipment for railroad locomotives and rolling stock, wherein a basic pulse train is transmitted whereof the pulses are of a selected first amplitude and represent a train axle count.
BookDOI
Finding Groups in Data
TL;DR: In this article, an electrical signal transmission system for railway locomotives and rolling stock is proposed, where a basic pulse train is transmitted whereof the pulses are of a selected first amplitude and represent a train axle count, and a spike pulse of greater selected amplitude is transmitted, occurring immediately after the axle count pulse to which it relates, whenever an overheated axle box is detected.
Journal ArticleDOI
Gene Selection for Cancer Classification using Support Vector Machines
TL;DR: In this article, a Support Vector Machine (SVM) method based on recursive feature elimination (RFE) was proposed to select a small subset of genes from broad patterns of gene expression data, recorded on DNA micro-arrays.