MABGCORRECT procedure

Performs background correction of Affymetrix slides (D.B. Baird).


Options

PRINT = string
What to print (quantiles); default quan

METHOD = string
Method of establishing grid background (mean, quantile); default mean

WEIGHTING = string
Weighting method to use (affymetrix, distance); default affy

POWER = scalar
Power applied to distance; default 2 i.e. square

SMOOTH = scalar
Smoothing parameter applied to weights; default 100


Parameters

DATA = variates
Data values

SLIDES = factors
Defines the slides

ROWS = factors
Defines the rows within each slide

COLUMNS = factors
Defines the columns within each slide

NEWDATA = variates
Saves the corrected values; if unset, they replace the original DATA values


Description

MABGCORRECT performs background correction of Affymetrix slides (or chips). The chip is divided into 16 zones in a 4 × 4 grid, and each spot has a weighted average of these 16 levels removed from it. The levels used are controlled by the METHOD options, with settings:

    means
the means of the values below the 2% quantile are used as the background levels; and

    quantiles
the actual 2% quantiles are used as the background levels.

The WEIGHTING option controls how the background levels are combined before removing them from each spot:

    affymetrix
the weights are 1/(dn + s), and

    distance
the weights are 1/(min(dn, s),

where d is the distance from the spot to the zone centroid, the power n is defined by the POWER option (default 2), and the smoothing parameter s is defined by the SMOOTH option (default 100).

   The data values are supplied, in a variate, by the DATA parameter. The SLIDES parameter supplies a factor to index the slides, and the ROWS and COLUMNS parameters supply factors to identify the rows and columns within each slide. The corrected values can be saved in a variate supplied by the NEWDATA parameter; if this is not set, the corrected values replace the original value in the DATA variate.

 

Options: PRINT, METHOD, WEIGHTING, POWER, SMOOTH.

Parameters: DATA, SLIDES, ROWS, COLUMNS, NEWDATA.