For an overview of outlier detection, please see the
corresponding section in the vignette Advanced topics: Customizing arrayQualityMetrics
reports and programmatic processing of the output.
These two functions are helper functions used by the different report
generating functions, such as
A matrix whose columns correspond to arrays, rows to the array features.
A character string specifying the summary statistic to
be used for each column of
A vector of real numbers.
A number is called an outlier if it is larger than the
upper hinge plus
outliers: with argument
method="KS", the function first
computes for each column of
exprs (i.e. for each array)
the value of the
ks.test test statistic
between its distribution of intensities and the pooled distribution of
intensities from all arrays.
"upperquartile", it computes the sum or
the 75 percent quantile. Subsequently, it calls
on these values to identify the outlying arrays.
boxplotOutliers uses a criterion similar to that used in
detect outliers in a set of real numbers. The main difference is that
boxplotOutliers, only the outliers to the right
(i.e. extraordinarily large values) are detected.
outliers, an object of class
boxplotOutliers, a list with two elements:
thresh, the threshold against which
x was compared, and
outliers, an integer vector of indices.
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