For each technology platform, we computed the Pearson's correlations and Spearman's rank correlations between the ratios across pairs of samples.
Because there are considerable technical variations between platforms, we restricted platforms to only the Affymetrix Human Genome U133 series.
To measure the compatibility between these platforms we compared overlapping SNP data from each pair of platforms.
To avoid complications from the comparison between different platforms, we only used measurements from the Affymetrix ATH1 GeneChip platform.
To avoid underestimating the computed correlation as a consequence of intrinsic differences between cell subpopulations, we computed a weighted Spearman correlation using the R package wCorr44.
Furthermore, in order to predict synergistic interactions between the regulators, we computed the enrichment of co-regulons.
To compare the microRNA profile between two different microarray platforms, we used all overlapped microRNAs available in both microarray platforms.
In order to show the speedups, we computed them with respect to each platform.
Using the designated normalization controls/probes for each array, we computed the intra- and inter-platform reproducibility.
First, we computed the correlation coefficients between three independent trials.
