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From the third issue of 2017, Microarrays has changed its name to High-Throughput.

Open AccessArticle

Assessing Agreement between miRNA Microarray Platforms

Department of Clinical Sciences and Community Health, University of Milan, Via Vanzetti 5 20133, Milano (MI), Italy
Author to whom correspondence should be addressed.
Microarrays 2014, 3(4), 302-321;
Received: 3 July 2014 / Revised: 24 September 2014 / Accepted: 25 November 2014 / Published: 12 December 2014
(This article belongs to the Special Issue Advances in Data Analysis Methods and Tools)
PDF [1389 KB, uploaded 12 December 2014]


Over the last few years, miRNA microarray platforms have provided great insights into the biological mechanisms underlying the onset and development of several diseases. However, only a few studies have evaluated the concordance between different microarray platforms using methods that took into account measurement error in the data. In this work, we propose the use of a modified version of the Bland–Altman plot to assess agreement between microarray platforms. To this aim, two samples, one renal tumor cell line and a pool of 20 different human normal tissues, were profiled using three different miRNA platforms (Affymetrix, Agilent, Illumina) on triplicate arrays. Intra-platform reliability was assessed by calculating pair-wise concordance correlation coefficients (CCC) between technical replicates and overall concordance correlation coefficient (OCCC) with bootstrap percentile confidence intervals, which revealed moderate-to-good repeatability of all platforms for both samples. Modified Bland–Altman analysis revealed good patterns of concordance for Agilent and Illumina, whereas Affymetrix showed poor-to-moderate agreement for both samples considered. The proposed method is useful to assess agreement between array platforms by modifying the original Bland–Altman plot to let it account for measurement error and bias correction and can be used to assess patterns of concordance between other kinds of arrays other than miRNA microarrays. View Full-Text
Keywords: miRNA microarray; reliability; agreement; Bland–Altman; measurement error miRNA microarray; reliability; agreement; Bland–Altman; measurement error

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Bassani, N.P.; Ambrogi, F.; Biganzoli, E.M. Assessing Agreement between miRNA Microarray Platforms. Microarrays 2014, 3, 302-321.

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