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By using the QC cutoff criteria, the inter-array variability, as assessed by the coefficient of variation in the expression levels for 100 maintenance genes, decreased significantly.
Expression levels for the 100 maintenance genes showed significantly greater variability among the 10 samples failing QC criteria ("fail" data set) than among the 10 samples passing QC criteria ("pass" data set, Figure 5).
Coefficient of variation analysis was used to determine variability in expression levels for each of the 100 maintenance genes across the 10 samples failing QC criteria and across 10 samples passing QC criteria.
Expression data for 100 maintenance gene probe sets on the array demonstrates that among the samples failing QC criteria, there is greater variability among reported expression levels for maintenance genes compared to randomly selected samples passing the QC criteria.
By independent linear regression, there was no correlation of gene expression level for the 100 maintenance genes (r<0.05 for all genes) with age (average 45 ± 8.8) across the 144 individuals from whom airway epithelium was derived.
To assess whether the gene expression data derived from samples that pass all of the QC criteria was more robust than that derived from samples that failed one or more conditions, for every sample, regardless of QC metric values, expression levels were extracted for the 100 maintenance genes.
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