QNORMALIZE procedure

Performs quantile normalization (D.B. Baird).


Options

PRINT = string
What to print (summary); default summ

PLOT = strings
What to plot (cdf, histogram, ncdf, nhistogram); default hist, nhis

METHOD = string
Whether to use means, medians or geometric means for the averaged normalized distribution (means, medians, geometricmeans); default mean

ARRANGEMENT = string
Whether to use trellis or single plots for PLOT=cdf or ncdf (single, trellis); default trel

DEVICE = scalar
Device number on which to plot the graphs

GRAPHICSFILE = text
What graphics filename template to use to save the graphs; default *


Parameters

DATA = variates or pointers
Data values

GROUPS = factors
Groupings of the data values

NEWDATA = variates
Saves the normalized values; if this is unset, they replace the original values in DATA


Description

QNORMALIZE performs quantile normalization. This transforms the data so that each group has a common cumulative density function. The data values are specified by the DATA parameter. They can be in a single variate, with groupings specified by the GROUPS parameter. Alternatively, they can be in separate variates, one for each group. The normalized values can be saved using the NEWDATA parameter. If this is not set, they replace the values in the DATA variate(s).

   The METHOD option selects the way in which the overall distribution is produced from the cumulative density functions within each group, with settings:

    means
takes the means;

    medians
takes the medians; and

    geometricmeans
takes geometric means (i.e. the mean on the log scale, back-transformed to the natural scale).

   The PLOT option controls what plots are produced: histograms or cumulative density plots of the original or normalized data. By default the plots for the groups are displayed in a trellis arrangement, but you can set option ARRANGEMENT=single to display them separately, in single plots. You can use the DEVICE option to plot to a device other than the screen. The GRAPHICSFILE option specifies then supplies a template for the file names.

   By default a summary is produced, giving quantiles by groups. This can be suppressed by putting option PRINT=*.

 

Options: PRINT, METHOD, ARRANGEMENT, DEVICE, GRAPHICSFILE.

Parameters: DATA, SLIDES, NEWDATA.


Action with RESTRICT

Any restrictions on the DATA variates are removed.