sscore (version 1.44.0)

computeOutlier: Compute outlier probes

Description

Computes outlier and/or mask probes for a set of Affymetrix GeneChips that will be excluded from S-Score calculations

Usage

computeOutlier(afbatch, rm.mask = TRUE, rm.outliers = TRUE, rm.extra = TRUE, celfile.path = NULL, celfile.names = NULL)

Arguments

afbatch

An AffyBatch object

rm.mask

should the spots marked as 'MASKS' be excluded from S-Score calculation?

rm.outliers

should the spots marked as 'OUTLIERS' be excluded from S-Score calculation?

rm.extra

if TRUE, overrides what is in rm.mask and rm.outliers

celfile.path

character denoting the path for the *.CEL files corresponding to afbatch

celfile.names

optional character vector containing the names of the *.CEL files

Value

a matrix containing the list of outliers / masked values for the given AffyBatch object.

Details

Computes the outlier and / or mask probes for an AffyBatch object. These are returned in matrix form, with one probe per row and one chip per column. The value of each location in the matrix will be TRUE if the corresponding probe is an outlier / masked value and FALSE if it is not. The options may be set to exclude only outlier values, only mask values, or both. The probes are be arranged in the same row order as the intensity values. Note that this function assumes the *.CEL files are still available in the directory given by celfile.path (or the current directory if celfile.path is not specified). The *.CEL names are given by celfile.names. If celfile.names is not specified, the sample names from the AffyBatch object will be used.

Examples

  if (length(dir(pattern=".cel$")) != 0) {
  abatch <- ReadAffy()
  outlier <- computeOutlier(abatch)
}