fixOutliers:
'Fix' an RGList object with outlying values.
Description
Imputes outlying values in one of the red foreground, red background,
green foreground, or green background matrices of an RGList
object created from Miltenyi Biotech miRXplore Microarrays.
Uses the replicate structure of the array to impute the outlying
values. Implicit assumption is that only
one of the four replicated values for a probe is an outlying value.
Usage
fixOutliers(mat, idx, gene.ids)
Arguments
mat
One of the red foreground (R), red background (Rb),
green foreground (G), or green background (Gb)
matrices in an RGList object, which contains
outlying values.
idx
Index of outlying values, as returned by the
checkOutliers function. See examples for usage.
gene.ids
Vector of gene IDs for each probe. See examples for usage.
Value
Returns a matrix with the outlying probe values imputed.
Details
The function is specific to RGList objects which were created
from Miltenyi Biotech miRXplore Microarrays,
since it depends on the replicated
structure of that array (probes spotted in quadruplicate) to impute
the outlying probe values.