PMC:4979053 / 19333-21825
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":"3.1. Data Description\nAnalyses involved two samples (A498, a tumor line, and hREF, a pool of healthy tissues), each with three technical replicates for all platforms considered (Affymetrix GeneChip© miRNA Array, Agilent Human miRNA Microarray (V1) and Illumina humanMI_V2). MiRNA selection described in the Experimental Section, resulted in a total of 813 human miRNAs considered for analysis, which account for 95.99% of human miRNAs on Affymetrix platforms, 95.53% on Agilent and 94.76% on Illumina (see Figure 1). Pairwise intersections of human miRNA lists revealed that the larger overlap occurred when Affymetrix and Agilent were considered (830 miRNAs, 97.99% of Affymetrix hsaand 97.53% of Agilent hsa), whereas Illumina showed a slightly poorer degree of overlap with both Affymetrix (817 miRNAs, 96.46% of Affymetrix and 95.22% of Illumina) and Agilent (815 miRNAs, 95.77% of Agilent and 94.99% of Illumina).\nFigure 1 Venn diagram of common human miRNAs across platforms. Density plots and boxplots for both samples in Figure 2 showed that the distribution of intensity values of common miRNAs was very different between platforms, with a marked skewness for Affymetrix and Agilent (red and green) and peaks of density for relatively low values. The Illumina platform was characterized by a slightly more symmetrical behavior. Notably, the first replicate of sample A498 had some technical problems for both Affymetrix and Agilent (solid red and green lines, lower right panel), whereas no similar pattern was seen for Illumina. In fact, the quantile distribution appeared to be quite different between technical replicates for these two platforms, despite similar inter-quartile ranges (see Table 1), suggesting that systematic bias had occurred in the profiling of the sample. The same plots were produced for normalized data and showed quite a different distribution, at least in terms of location, in particular for Illumina platform, whose right tail was relevantly reduced (see Supplementary Material, Figures S1 and S2).\nmicroarrays-03-00302-t001_Table 1 Table 1 Quartiles and inter-quartile range for the three platforms.\nFigure 2 Box and density plots for both samples. The left column refers to hREF and the right column to A498. Plots refer to non-normalized log2-transformed data. (Lower panels) Solid lines represent the technical replicate labeled as 1 in the datasets, whereas dashed lines and dotted lines represent technical Replicate 2 and 3, respectively.\n\n3","divisions":[{"label":"Title","span":{"begin":0,"end":21}},{"label":"Figure caption","span":{"begin":919,"end":984}},{"label":"Table caption","span":{"begin":2041,"end":2145}},{"label":"Figure caption","span":{"begin":2144,"end":2491}}],"tracks":[]}