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Table 2 Affymetrix Expression Console Quality Control Statistics (Exon Arrays)

From: Unsupervised assessment of microarray data quality using a Gaussian mixture model

Quality Statistic1

Description

pm.mean

mean of the raw intensity for all PM probes, prior to any normalizations.

bgrd.mean

mean of the raw intensity for all probes used to compute background intensity. (Note: may be higher than pm.mean because GC compositions of probes used to compute background and PM probes can be quite different.)

pos.vs.neg.auc

area under ROC curve discriminating between positive control probesets and negative control probesets.

probeset.mean, probeset.stdev

mean and standard deviation of probeset signals after normalization. 2

probeset.mad.residual.mean, probeset.mad.residual.stdev

mean and standard deviation of the absolute deviations of the RMA probe level model residuals from the median across chips. 2

probeset.rle.mean, probeset.rle.stdev

mean and standard deviation of the absolute values of the relative log expression (RLE) for all probesets. 2

  1. 1. The "SCORE" function was used to normalize values for each statistic, t, for each chip, i, relative to the values observed in other chips from the same experiment: ; with median() and mad() computed across all chips in the experiment.
  2. 2. Separate statistics are computed for a) all probesets, b) negative control probesets, and c) positive control probesets.