Figure 2

Replicate scatter plots comparing total RNA for replicates 1 (a, c, e) and 3 (b, d, f) against the artefact-free replicate 2 for the exon array measurement in DG75-10/12 cells. Subfigures a and b show the results using both RMA and quantile normalization, c and d using only RMA without quantile normalization and E and F after probe correction. Probesets are colored according to the percentage of their probes that are flagged as corrupted according to the ε-criterion based on the noise scores calculated using newly transcribed and pre-existing RNA as control. For replicate 1 there is a bias even for the uncorrupted probesets (a) that can be reduced by omitting quantile normalization (c). If probe correction is applied prior to normalization and summarization (e,f), this bias is removed. Here, the results are shown for the correction method which replaces the probe value by the mean of the unaffected probes in the same probe set. In this case, the intensity of probesets for which all probes are corrupted are set to zero. Results for the filtering approach in which affected probes are removed from the probeset definition are very similar.