Abstract
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.
Highlights
MiRNAs are small non-coding RNA molecules that have been shown to play a critical role in tumorigenesis [1,2,3,4] and in several other pathologies [5,6,7,8]
To assess the reliability of the three miRNA microarray platforms, pair-wise concordance correlation coefficients [17] were computed for all possible pairs of technical replicates for all platforms, within each sample
It can be noticed that estimates were mostly unchanged for the Illumina platform, though with a slight improvement after data filtering, whereas for Agilent, the pattern was not clear, though the differences appeared to be larger for A498, where filtering led to some relevant improvements, both in the pair-wise correlation coefficients (CCC) and in the overall concordance correlation coefficient (OCCC)
Summary
MiRNAs are small non-coding RNA molecules that have been shown to play a critical role in tumorigenesis [1,2,3,4] and in several other pathologies [5,6,7,8]. Since results from these comparison studies appear to be contrasting, miRNA microarrays still remain an effective and useful technology, whose characteristics need to be properly assessed, both in terms of within-platform reliability and of between-platforms agreement. Sato and colleagues assessed between-platform comparability in terms of miRNAs that were commonly differentially expressed between samples for all platforms [15], whereas Yauk et al [16] evaluated within-platform reproducibility via Lin’s concordance correlation coefficient [17]. The proposed method is applied to assess agreement between three different miRNA microarray platforms (Affymetrix, Agilent, Illumina). Advice against the use of Pearson/Spearman correlation coefficients is provided, and use of concordance correlation coefficients (pairwise and overall) is suggested as a better measure to evaluate within-platform reliability
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