PMC:4979053 / 6170-7561 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/4979053","sourcedb":"PMC","sourceid":"4979053","source_url":"https://www.ncbi.nlm.nih.gov/pmc/4979053","text":"2.3.1. Affymetrix GeneChip© miRNA Array\nIntensity .CEL files were obtained from the scan images and imported to the Affymetrix© miRNA QC Tool software (Version 1.0.33.0) to quantify the signal value. Quality control (QC) was assessed by plotting the average intensity of the oligo spike-in and background probe sets (included in the control target content) across all of the arrays. According to Genisphere, oligo spike-in 2, 23, 29, 31 and 36 probe sets should present a value of more than 1000 intensity units to accept array quality. The miRNA arrays were detected using the Affymetrix detection algorithm, based on the non-parametric Wilcoxon rank-sum test, applied independently on each array and probe/probe set; a p-value greater than 0.06 stands for “not detected above background” [19]. For data normalization, the “default” method was used, obtaining log2 expression values (expression values data matrix) from the raw data (intensity values data matrix). Briefly, this method involved the following three steps: grouping the background probes intensities based on GCcontent, where the median intensity of each bin was the correction value for each probe with the same GC content; a quantile normalization and, finally, a median polish summarization. To obtain a single intensity value for each miRNA mapped on the log2 array, intensity measures for replicated spots were averaged.","divisions":[{"label":"Title","span":{"begin":0,"end":39}}],"tracks":[]}