Are clusters found in one dataset present in another dataset?

Biostatistics
Amy V Kapp, Robert Tibshirani

Abstract

In many microarray studies, a cluster defined on one dataset is sought in an independent dataset. If the cluster is found in the new dataset, the cluster is said to be "reproducible" and may be biologically significant. Classifying a new datum to a previously defined cluster can be seen as predicting which of the previously defined clusters is most similar to the new datum. If the new data classified to a cluster are similar, molecularly or clinically, to the data already present in the cluster, then the cluster is reproducible and the corresponding prediction accuracy is high. Here, we take advantage of the connection between reproducibility and prediction accuracy to develop a validation procedure for clusters found in datasets independent of the one in which they were characterized. We define a cluster quality measure called the "in-group proportion" (IGP) and introduce a general procedure for individually validating clusters. Using simulations and real breast cancer datasets, the IGP is compared to four other popular cluster quality measures (homogeneity score, separation score, silhouette width, and weighted average discrepant pairs score). Moreover, simulations and the real breast cancer datasets are used to compare the f...Continue Reading

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Citations

Oct 8, 2013·Breast Cancer Research and Treatment·Giovanni CirielloNikolaus Schultz
Mar 25, 2009·Clinical & Experimental Metastasis·Ulrich PfefferAdriana Albini
Jul 3, 2007·Journal of Chemical Information and Modeling·Rajarshi GuhaTing Chen
Nov 15, 2007·Journal of the National Cancer Institute·Lara LusaMarco A Pierotti
Dec 21, 2006·BMC Bioinformatics·Shuangge Ma
Sep 13, 2006·BMC Genomics·Amy V KappRobert Tibshirani
Feb 2, 2011·PLoS Computational Biology·Peter LangfelderSteve Horvath
Apr 28, 2012·PloS One·Ronglai ShenChris Sander
Jul 31, 2014·PloS One·Anna Dvorkin-Gheva, John A Hassell
Aug 5, 2011·Breast Cancer Research and Treatment·Oscar KrijgsmanAnnuska M Glas
Jan 27, 2012·Journal of the American Medical Informatics Association : JAMIA·Lee A D CooperJoel H Saltz
Nov 20, 2012·American Journal of Clinical Pathology·Kimberly H Allison
Mar 11, 2016·Genome Medicine·Catherine R Planey, Olivier Gevaert
May 1, 2013·Genes, Chromosomes & Cancer·Nanne K KloosterhofPim J French
Oct 17, 2015·Scientific Reports·Bing LiYongyan Wang
Jan 17, 2015·BMC Bioinformatics·Askar ObulkasimMark A van de Wiel
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Jun 13, 2019·Leukemia·Amjad AlkodsiSampsa Hautaniemi
Oct 30, 2019·Molecular Imaging and Biology : MIB : the Official Publication of the Academy of Molecular Imaging·Hui XuLijun Lu
May 28, 2020·Nature Communications·Isabel AlmudiFernando Casares

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