MABGCORRECT procedure

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

Options

PRINT = string token	What to print (quantiles); default quan
METHOD = string token	Method of establishing grid background (mean, quantile); default mean
WEIGHTING = string token	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 or pointers	Data values
SLIDES = factors or texts	Defines the slides
ROWS = factors	Defines the rows within each slide
COLUMNS = factors	Defines the columns within each slide
NEWDATA = variates or pointers	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 by the DATA parameter, either as a variate, or as a pointer containing a variate for each slide. If DATA specifies a variate containing data for several slides, the SLIDES parameter must supply a factor to index the slides, and the ROWS and COLUMNS parameters supply factors to identify the rows and columns within the slides. If DATA specifies a pointer, the SLIDES parameter can be omitted, or it can supply a text to label the slides in the pointer. The ROWS and COLUMNS parameters then supply factors to identify the rows and columns for an individual slide, and all the slides must have the same layout. The corrected values can be saved in a variate or pointer, supplied by the NEWDATA parameter; if this is not set, the corrected values replace the original values in DATA.

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

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

See also

Procedures: AFFYMETRIX, FDRBONFERRONI, FDRMIXTURE, MAANOVA, MAEBAYES, MAREGRESSION, MARMA, MAROBUSTMEANS, MAVDIFFERENCE, MAVOLCANO, QNORMALIZE.

Commands for: Microarray data.

Example

CAPTION       'MABGCORRECT example'; STYLE=meta
ENQUIRE       CHANNEL=-1; EXIST=check; NAME=\
              '%GENDIR%/Data/Microarrays/HybStds.gwb'
IF check
  SPLOAD      '%GENDIR%/Data/Microarrays/HybStds.gwb'
" Use 2% quantile of values with affymetrix weighting."
  MABGCORRECT [METHOD=quantiles; WEIGHTING=affymetrix; POWER=2] Intensity;\
              SLIDES=Slide; ROWS=ROW; COLUMNS=COL; NEWDATA=CIntensity
" Use means of lowest 2% of values with distance weighting,
  replacing original values."
  MABGCORRECT [METHOD=means; WEIGHTING=distance; POWER=1] Intensity;\
              SLIDES=Slide; ROWS=ROW; COLUMNS=COL
ELSE
  CAPTION     'Microarray example datasets have not been installed.'
ENDIF