QualityWeights: Spot Quality Weights

Description

Functions to calculate quality weights for individual spots based on image analyis output file.

Usage

wtarea(ideal=c(160,170))
wtflags(weight=0,cutoff=0)
wtIgnore.Filter

Arguments

ideal

numeric vector giving the ideal area or range of areas for a spot in pixels

weight

weight to be given to flagged spots

cutoff

cutoff value for Flags below which spots will be downweighted

Value

A function which takes a dataframe or matrix as argument and produces a numeric vector of weights between 0 and 1

Details

These functions can be passed as an argument to read.maimages to construct quality weights as the microarray data is read in. wtarea downweights unusually small or large spots and is designed for SPOT output. It gives weight 1 to spots which have areas in the ideal range, given in pixels, and linearly downweights spots which are smaller or larger than this range. wtflags is designed for GenePix output and gives the specified weight to spots with Flags value less than the cutoff value. Choose cutoff=0 to downweight all flagged spots. Choose cutoff=-50 to downweight bad or absent spots or cutoff=-75 to downweight only spots which have been manually flagged as bad. wtIgnore.Filter is designed for QuantArray output and sets the weights equal to the column Ignore Filter produced by QuantArray. These weights are 0 for spots to be ignored and 1 otherwise.

Examples

Run this code

#  Read in spot output files from current directory and give full weight to 165
#  pixel spots.  Note: for this example to run you must set fnames to the names
#  of actual spot output files (data not provided).
RG <- read.maimages(fnames,source="spot",wt.fun=wtarea(165))
#  Spot will be downweighted according to weights found in RG
MA <- normalizeWithinArrays(RG,layout)