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