Additional file 1.

Dose response plots of a representative 1X–5X data set. Panels a-d show the scatter plots of standardized natural log intensity of the 1X, 3X, 4X, and 5X samples relative to the 2X sample. Here, standardization refers to the following data transformation: standardized intensity of chromosome X probe = (intensity of chromosome X probe-mean intensity of the autosomal probes)/standard deviation of the intensity of autosomal probes. Red dots represent randomly selected chromosome X probes and black dots represent randomly selected autosomal probes. The blues lines are the Y = X lines. Panel e shows the relationship between the natural log-transformed intensity and the natural log-transformed copy number. Natural log-transformed mean intensity of all chromosome X probes from the 1X–5X samples are plotted on the Y-axis and natural log-transformed copy number are plotted on the X-axis. The blue line is the linear regression line using the natural log-transformed mean intensity as response and natural log-transformed copy number as predictors.

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Shen et al. BMC Genetics 2008 9:27   doi:10.1186/1471-2156-9-27