[BioC] ArrayQualityMetrics: Grey boxes in boxplot

[jeremy wilson]

Dear all,
I am noticing that some of my boxes in the boxplot are colored grey. I
looked at the code to plot the boxplots (aqm.boxplot) and observed
that there is a parameter "outlier" whose length if not zero  will
color the respective arrays as grey. These outliers as I understand
from the code are a union of outliers based on mean and variance of
intensity distributions. Just by looking at the boxplots (attached), I
do not think the 1st and the 5th arrays are outliers?
The thing is that these were not shown as outliers in the report with
a * mark in the before normalization report. The 9th array which is
shown as grey in the after normalization plot was shown as outlier (*)
when the eset after normalization was used to perform AQM.
Are the grey colored ones really outliers or some thing else? If they
are outliers, why are the three arrays from the before normalization
boxplot not marked as outliers in the report?

Please let me know
Thank you
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