Figure 3

Comparison of variance components in Affymetrix and Illumina data. Comparison of MAQC and Paterson Affymetrix variance components. A: Probe-wise SD-estimates corresponding to several levels of technical variance (see figure key) in detection-filtered and quantile normalised MCF7/MCF10 expressions from the Paterson Affymetrix dataset. B: Probe-wise estimates of standard deviations (SD) corresponding to the inter-experiment (light blue), inter-run (dark blue), and inter-chip (green) technical variance in our UHRR Illumina data. The effect on these standard deviations following detection-filtering (DF), quantile-normalisation (QN), ComBat batch-correction by experiment (CB(expt)), and ComBat batch-correction by run (CB(run)) are shown. C: Probe-wise SD-estimates corresponding to inter-laboratory (pale blue), inter-chip (green), and inter-array (dark green) technical variances in detection-filtered and quantile normalised UHRR/UBRR expressions from the MAQC Illumina dataset. D: Probe-wise SD-estimates corresponding to inter-laboratory (pale blue) and inter-chip (green) technical variances in detection-filtered and quantile normalised UHRR/UBRR expressions from the MAQC Affymetrix dataset.