PMC:4979053 / 21824-25647
Annnotations
{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/4979053","sourcedb":"PMC","sourceid":"4979053","source_url":"https://www.ncbi.nlm.nih.gov/pmc/4979053","text":"3.2. Intra-Platform Reliability\nResults for the pairwise CCCs and the overall CCC for each sample and platform using common human miRNAs are reported in Table 2. Globally, the hREF sample showed better features of reliability, in particular for the Agilent and Illumina platform (OCCC: 0.994 (CI 95%: 0.993–0.995) and 0.994 (CI 95%: 0.994–0.995), respectively). On the other hand, the A498 sample showed lower values of OCCC, which dramatically decreased when considering the Affymetrix platform (0.927, CI 95%: 0.906–0.941). According to the non-inferiority threshold of 0.96 defined in the Experimental Section, Agilent and Illumina could be consistently declared repeatable across the two samples considered, whereas Affymetrix resulted in repeatable only for sample hREF.\nAs a means of comparison to previous studies, these results were obtained also on data filtered using the detection call approach, i.e., by removing all of the miRNAs that were called “present” on no more than two samples (see Table 3). This information was available only for Agilent and Illumina and led to a reduced dataset consisting of 347 human miRNAs. 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 CCC and in the OCCC.\nmicroarrays-03-00302-t002_Table 2 Table 2 CCC and Overall CCC with bootstrap 95%CI (common miRNAs) CCCs and the OCCC were computed on the 813 miRNAs common across all platforms considered for the study, and bootstrap 95%CI for the Overall Concordance Correlation Coefficient were computed using 1000 bootstrap samples and the percentile method [32].\nmicroarrays-03-00302-t003_Table 3 Table 3 Concordance correlation coefficient (CCC) and overall CCC with bootstrap 95% CI (detection call filtering). CCCs and the OCCC were computed on the 347 miRNAs common across Illumina and Agilent platforms after detection call filtering (present on at least three samples), and bootstrap 95% CI for the overall CCC were computed using 1000 bootstrap samples and the percentile method [32]. CCCs and OCCC using all human miRNAs and all miRNAs (human and non-human) were also evaluated on each platform (see Supplementary Material, Tables S1 and S2). When considering all of the human miRNAs on each platform (847 for Affymetrix, 851 for Agilent and 858 for Illumina; Table S1), results were almost identical to the situation with only common miRNAs used, the only difference lying in the Affymetrix platform for sample A498, which showed an OCCC of 0.93 (CI 95%: 0.911–0.943), a slightly higher value than those seen for common miRNAs. Using all of the miRNAs measured on the platform (7815 for Affymetrix, 921 for Agilent and 1145 for Illumina) returned values that confirmed patterns of agreement already depicted in Table 2 and Table S1, with the exception of line A498 for Affymetrix, which showed an increase, both in point and interval estimates for the OCCC (0.954, CI 95%: 0.950–0.957, see Table S2). The Agilent platform on line A498, on the contrary, showed similar patterns of moderate-to-poor agreement throughout all miRNA selection strategies.\nAdditionally, the normalization effect was evaluated by estimating CCC and overall CCC on data normalized according to quantile and loess normalization [38], which resulted in a general increase of both pairwise and overall concordance for both samples and for all platforms. In particular, also sample A498 profiled with Affymetrix showed good patterns of repeatability, with its CI 95% lying above the threshold of 0.96. Detailed results were reported in Tables S3 and S4 of the Supplementary Material.","divisions":[{"label":"Title","span":{"begin":0,"end":31}},{"label":"Table caption","span":{"begin":1469,"end":1821}},{"label":"Table caption","span":{"begin":1820,"end":2251}}],"tracks":[{"project":"2_test","denotations":[{"id":"27600350-12538238-69476975","span":{"begin":3472,"end":3474},"obj":"12538238"}],"attributes":[{"subj":"27600350-12538238-69476975","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#cbec93","default":true}]}]}}