Methylation outliers (loci with very extreme values of the Meth or Unmeth channel) are identified and fixed (see details).
An object of class
The number of standard deviations away from the median when defining the outlier cutoff, see details.
Should the function be verbose?
This function fixes outlying methylation calls in the Meth channel and Unmeth channel separately.
Unlike other types of arrays, all loci on a methylation array ought to measure something (apart from loci on the Y chromosome in a female sample). An outlier is a loci with a very low value in one of the two methylation channels. Typically, relatively few loci ought to be outliers.
An outlier is defined in a sample and methylation channel specific
way. First the (sample, methylation channel) values are
log2(x+0.5) transformed and then the median and mad of these
values are computed. An outlier is then defined to be any value less
than the median plus
K times the mad, and these outlier values
are thresholded at the cutoff (on the original scale).
An object of the same class as
object where outlier values in
the methylation channels have been thresholded.
Rafael A. Irizarry and Kasper D. Hansen
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