'Fix' an RGList object with missing values.

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Description

Imputes missing 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 missing values. Implicit assumption is that only one of the four replicated values for a probe is an missing value.

Usage

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fixMVs(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 missing values.

idx

Index of missing values, as returned by the checkMVs 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 missing probe values.

Value

Returns a matrix with the missing probe values imputed.

See Also

checkMVs, checkOutliers, fixOutliers

Examples

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data(PalateData)
mvs <- checkMVs(PalateData)
PalateData$Rb <- fixMVs(PalateData$Rb, mvs$Rb.na, PalateData$genes$Gene)