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# MAVDIFFERENCE procedure

Applies the average difference algorithm to Affymetrix data (D.B. Baird).

### Options

`PRINT` = string token Whether to print monitoring information (`monitoring`); default `*` Maximum number of iterations; default 50

### Parameters

`DATA` = variates or pointers Data values Groupings of the data values Saves the means Saves standard errors

### Description

`MAVDIFFERENCE` uses the average difference algorithm to remove extreme values from Affymetrix data. These are defined as values more than option `SDLIMIT` standard deviations from the mean.

The data values are specified by the `DATA` parameter. They can be in a single variate, with any groupings (corresponding to different genes or probes) specified by the `GROUPS` parameter. Alternatively, they can be in separate variates, one for each group. The `MEANS` parameter saves the means. The `SE` parameter saves the estimated standard deviation when there are no groups, or the standard error of the mean when there are groups.

Options: `PRINT`, `SDLIMIT`.

Parameters: `DATA`, `GROUPS`, `MEANS`, `SE`.

### Action with `RESTRICT`

`MAVDIFFERENCE` takes account of any restrictions on `DATA` or `GROUPS`.

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

Commands for: Microarray data.

### Example

```CAPTION         'MAVDIFFERENCE example'; STYLE=meta
ENQUIRE         CHANNEL=-1; EXIST=check; NAME=\
'%GENDIR%/Data/Microarrays/HybStds.gwb'
IF check
"Convert Data into PM/MM columns"
SORT          [INDEX=Slide,Probe,Atom] Slide,Probe,Atom,PM_MM,Intensity
SUBSET        [PM_MM .in. 'MM'] Intensity; MM
SUBSET        [PM_MM .in. 'PM'] Slide,Probe,Atom,Intensity
CALCULATE     PM = Intensity
DELETE        [REDEFINE=yes] Intensity,ROW,COL,PM_MM
FACPRODUCT    !p(Slide,Probe); SlideProbe
CALCULATE     LogDiff = (LOG(PM) - LOG(MM))/LOG(2)
MAVDIFFERENCE [PRINT=Monitoring] LogDiff; GROUPS=SlideProbe;\
MEANS=ESTIMATES; SE=SE
"Extract Labels for combined factor and split into two parts"
GETATTRIBUTE  [ATTRIBUTE=labels] SlideProbe; SPLabs
TEXT          Slide_Probe; SPLabs['labels']
CALCULATE     Space_Pos = GETPOSITION(Slide_Probe;' ')
CONCATENATE   [NEWTEXT=SlideID] Slide_Probe; WIDTH=Space_Pos-1
CONCATENATE   [NEWTEXT=ProbeID] Slide_Probe; SKIP=Space_Pos

"Display results"