Hi,
I am checking the quality of my array datasets using arrayQualityMetrics and it has not detected any outlier. However, in the figure (Variance mean dependence) captions, it is written that "Figure shows a density plot of the standard deviation of the intensities across arrays on the y-axis versus the rank of their mean on the x-axis. The red dots, connected by lines, show the running median of the standard deviation. After normalisation and transformation to a logarithm(-like) scale, one typically expects the red line to be approximately horizontal, that is, show no substantial trend. In some cases, a hump on the right hand of the x-axis can be observed and is symptomatic of a saturation of the intensities."
What is meant by intensity saturation and is my figure looks alright? I can also see the hump, but not sure if that is what they mean by intensity saturation?
Thank you in advance.
