Quality Control

Scale Factor
Scale factor for an Affymetrix chip is the ratio between the trimmed mean of the expression values for that chip and the target intensity (in our case 100). A similar value was computed for the non-Affymetrix chips (target intensity/ median expression value)
Percent Present
Percent Present is the number of probes called present on the array divided by the total number of probes. A description of how calls were generated for non-Affymetrix chips is detailed in the normalization section.
53 Ratios
For Affymetrix chips, the GapDH and Beta Actin 53 ratios were computed based on MAS5 expression values.
QC Metric Distributions
While no hard cutoffs were applied for each of the QC metrics, we examined the distribution of the metrics to determine if samples appeared to be outliers.
Principal components analysis (PCA) and clustering were used to visualize the relationship between the samples and determine if one or more samples appeared to be outliers.