A compendium to ensure computational reproducibility in high-dimensional classification tasks

Statistical Applications in Genetics and Molecular Biology
Markus RuschhauptUlrich Mansmann

Abstract

We demonstrate a concept and implementation of a compendium for the classification of high-dimensional data from microarray gene expression profiles. A compendium is an interactive document that bundles primary data, statistical processing methods, figures, and derived data together with the textual documentation and conclusions. Interactivity allows the reader to modify and extend these components. We address the following questions: how much does the discriminatory power of a classifier depend on the choice of the algorithm that was used to identify it; what alternative classifiers could be used just as well; how robust is the result. The answers to these questions are essential prerequisites for validation and biological interpretation of the classifiers. We show how to use this approach by looking at these questions for a specific breast cancer microarray data set that first has been studied by Huang et al. (2003).

Citations

Dec 14, 2011·Neuroradiology·Katrin HaeglerJennifer Linn
Jun 20, 2006·Mammalian Genome : Official Journal of the International Mammalian Genome Society·Christina Kendziorski, Ping Wang
Jan 1, 2010·BMC Bioinformatics·Andreas BunessAchim Tresch
Jan 21, 2006·BMC Bioinformatics·Hongbo ZhuThomas Lengauer
Aug 24, 2006·BMC Bioinformatics·Jochen Jaeger, Rainer Spang
Nov 17, 2007·Chemistry Central Journal·Andreas Steffen, Joannis Apostolakis
May 15, 2010·Genome Medicine·Katie MoyerJorge A Bezerra
Jan 15, 2008·Gynecologic Oncology·Petra BiewengaFrank Baas
Dec 11, 2008·Biometrical Journal. Biometrische Zeitschrift·Holger SchwenderJörg Rahnenführer
Jul 30, 2008·Biometrical Journal. Biometrische Zeitschrift·Thomas A GerdsMartin Schumacher
Feb 4, 2012·American Journal of Transplantation : Official Journal of the American Society of Transplantation and the American Society of Transplant Surgeons·L LiM M Sarwal
Apr 3, 2014·Journal of Bone and Mineral Research : the Official Journal of the American Society for Bone and Mineral Research·Todd L BredbennerUNKNOWN Osteoporotic Fractures in Men (MrOS) Study
Oct 19, 2006·Journal of the American College of Cardiology·Andreas S BarthHolger Sültmann
Nov 1, 2006·Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology·André OberthuerMatthias Fischer
Feb 15, 2011·Nucleic Acids Research·Joëlle VermeulenJo Vandesompele
Jan 10, 2017·MSystems·Aaron WeimannAlice C McHardy
May 25, 2006·International Journal of Cancer. Journal International Du Cancer·Joern GroeneAndré Rosenthal
Oct 5, 2006·International Journal of Cancer. Journal International Du Cancer·Jörg SchneiderHolger Sültmann
Jan 10, 2013·Source Code for Biology and Medicine·Guy N BrockM Michele Pisano
Mar 3, 2006·American Journal of Epidemiology·Roger D PengScott L Zeger
Jan 1, 2008·Cancer Informatics·A-L BoulesteixM Daumer
Feb 9, 2010·Bioinformatics and Biology Insights·Markus SchmidbergerUlrich Mansmann
Oct 28, 2011·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Katleen De PreterJo Vandesompele
Jan 24, 2006·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Daniel E StangePeter Lichter
Feb 5, 2009·Cancer Epidemiology, Biomarkers & Prevention : a Publication of the American Association for Cancer Research, Cosponsored by the American Society of Preventive Oncology·Charles J RosserSteve Goodison
Feb 25, 2010·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Katleen De PreterJo Vandesompele
Oct 8, 2020·Neuropsychopharmacology : Official Publication of the American College of Neuropsychopharmacology·Shalaila S HaasLana Kambeitz-Ilankovic
Aug 13, 2020·Biological Psychiatry·David PopovicUNKNOWN PRONIA Consortium

❮ Previous
Next ❯

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.