Figure 5

The effect of including poor quality chips in analyses on ability to detect differential gene expression. Fewer differentially expressed genes are detected when comparing male and female motor cortex if a chip that failed QC is included in the analysis, reflected in the at least 50% fewer probe sets detected as differentially expressed at the two different p-value thresholds (t-test nominal unadjusted p-values). Bad (B) indicates comparisons where one chip that failed QC (HC71: female) was included in the analysis; Good (G) indicates comparisons where all chips passed QC. Samples were matched for age. This effect is most marked with very small chip numbers and gradually becomes less as chip numbers increase.