Relative impact of key sources of systematic noise in Affymetrix and Illumina gene-expression microarray experiments.

Taking this further, we correlated probe GC-fraction with error estimates from the Ref-8/HT-12 UHRR replicates (Figure 3B ), revealing highly significant enrichment for higher standard deviations (SD) at lower GC-fractions (< 0.55) at the inter-experiment (Figure 6A -bottom; χ 2 pVal < 5.3 * 10 -8 ) and inter-run (Figure 6B -bottom; χ 2 pVal < 2.2 * 10 -16 ) levels, but not at the inter-chip level (Figure 6C -bottom).

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