PMC:3807239 / 12365-15559 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/3807239","sourcedb":"PMC","sourceid":"3807239","source_url":"https://www.ncbi.nlm.nih.gov/pmc/3807239","text":"3. Intra- and Inter-Platform Reproducibility\nThe diversity of platforms and analytical methods have made cross-platform microarray data comparison and integration challenging. Agreement in results obtained with different platforms have been observed in some comparison studies [21,22,23,24,25,26], while others have not [27,28,29,30]. Various studies tackled the issue of reproducibility of cDNA microarrays across platforms and between laboratories [31,32,33,34,35]. Results showed that the correlation between the two datasets from the Affymetrix platform and the spotted cDNA platform is poor when the ratios and the spot intensities are compared [27,35,36]. The cross-platform reproducibility can be much improved by using standardized protocols [34]. Further, across-laboratory comparisons showed that the reproducibility for a platform within a single laboratory is good, and the data from the best-performing labs agree with each other rather well [31,32]. Using probe sequences matched at the exon level, the consistency of measurements across the different platforms can be improved compared with annotation-based matches [33]. This confirmed the conjecture that the discrepancies might be due to the different array types measuring different variants of the same gene.\nMature miRNAs are short, many of which are approximately 20 nuclides in length. As a result, the inconsistency of measurements caused by annotation-based matches across different miRNA microarray platforms won’t be as severe as those across different mRNA/cDNA microarray platforms. However, the short lengths of the miRNAs will cause a wide Tm range within the entire miRNA population, which results in binding efficacy or fluorescent distortion. This will ultimately influence the sensitivity of different platforms and, hence, make the cross-platform data comparison and data integration a challenge. Kuo et al. compared nearly all available commercial and “in-house” platforms and found that the concordance of measurements was lower across platforms than between laboratories on the same platform. In addition, the consistency of low expression miRNAs was lower than that of high expression miRNAs [31,32,33,34,35].\nWe investigated the intra-platform reproducibility by comparing the Spearman’s correlation coefficients among various miRNA profiles tested on different samples using the same platforms for LNAv9, FlexmiR bead array and TLDA, respectively. Results showed that the bead array has the highest intra-platform reproducibility with a median coefficient of 0.8544 and a standard deviation 0.0475. TLDA and LNAv9 also have reasonable high intra-platform reproducibility, with median coefficients of 0.8118 and 0.7367, respectively. The inter-platform reproducibility between TLDA and the bead array is low, with a median of 0.1060 and a standard deviation of 0.0391. While LNAv9 has relatively higher inter-platform reproducibility with the TLDA (with a median of 0.4872 and a standard deviation of 0.0962) and with bead array (with a median of 0.4521 and a standard deviation of 0.0537) [37]. Overall, the inter-platform reproducibility is much lower compared with the intra-platform 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