Figure 2.

Quantile-quantile plots and density plots for HGU95 Spike-In data. (a) Quantile-quantile plot with quantiles of the standard normal distribution on the horizontal axis and quantiles of the noise distribution as estimated by the exponential-normal convolution model. If the normality assumption is correct, the plotted values should lie on a straight line. (b) Quantiles of an exponential distribution versus the background corrected probe-level intensities from the exponential-normal model. Again, any departures from a straight line indicate a lack of fit for the exponential distribution. (c) Density estimates of the log base 2 PM intensities for the original (uncorrected) probe-level intensities (solid line) and the estimated background using the exponential-normal model (dashed line). (d) Density estimates of the log base 2 PM intensities from the original data versus a simulated convolution of a normal distribution and an exponential distribution. The parameters for the normal and exponential distributions were obtained using estimates given by the Bioconductor implementation of RMA.

Chen et al. BMC Genomics 2009 10(Suppl 1):S19   doi:10.1186/1471-2164-10-S1-S19