Scatter plots of the Cy5 versus Cy3 channels for 50-mer probes from  with (a) 28256_Input versus 28256_ChIP for G+C = 11 bases and (b) 28256_Input versus 28256_ChIP for G+C = 39 bases. The correlation is 0.364 in (a) and 0.860 in (b). (c) Plot of the inter-channel correlation (28256_Input, 28256_ChIP) across GC bins within the same array. The higher GC-count probes are more correlated and, therefore, should be more reliable in detecting differentially expressed or enriched probes. That is, in ChIP-chip, more than 99% of probes just measure the background and, thus, should ideally give similar results for the two channels. The correlation between the two channels, however, depends on the GC content of the probes. Since the two-channel correlation for high-GC probes is much higher than that for low-GC probes, significant two-channel fold-changes in the former category are much more reliable than those in the latter category, where large fold-changes may readily occur by chance.
Song et al. Genome Biology 2007 8:R178 doi:10.1186/gb-2007-8-8-r178