When Quantile Normalization is selected for microarray data, ArrayStar adjusts the probe intensity data in two steps:
1) Probe intensity values are adjusted so that the distribution is the same across all arrays.
2) Probe data are summarized into gene level signal values, using the selected summarization method: Averaging (the geometric mean of probe intensity values is used), or Median Polish.
When Quantile is selected for RNA-Seq data, ArrayStar adjusts the signal values for each experiment in your project so that the distribution is the same across each experiment. In this case, there is no summarization step.