The Illumina BeadStudio [15 (link)] output file was processed using the lumi package available in Bioconductor software collection [16 (link)]. The processing included the following steps: quality control of raw data; background subtraction; and variance stabilization using algorithm VST, developed for Illumina data. Values after this processing step should be treated as log-transformed.
Quantile normalization was performed. First, pairwise correlations of intensities were consistently high (>0.95) for the samples. Additionally, we excluded all probes that had detection p-value > 0.05 in all 3 samples. A total of 4 columns (samples) and 11,073 rows (probes) corresponded to 9659 non-redundant genes. Fold changes in gene expression relative to the expression in the control sample were calculated.
Quantile normalization was performed. First, pairwise correlations of intensities were consistently high (>0.95) for the samples. Additionally, we excluded all probes that had detection p-value > 0.05 in all 3 samples. A total of 4 columns (samples) and 11,073 rows (probes) corresponded to 9659 non-redundant genes. Fold changes in gene expression relative to the expression in the control sample were calculated.
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