'Fix' an RGList object with outlying values.

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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

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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.

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.

Value

Returns a matrix with the outlying probe values imputed.

See Also

checkOutliers, checkMVs, fixMVs

Examples

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data(PalateData)
outliers <- checkOutliers(PalateData)
PalateData$R <- fixOutliers(PalateData$R, outliers$Rout, PalateData$genes$Gene)