Performs quantile normalization (D.B. Baird).

### Options

`PRINT` = string token |
What to print (`summary` ); default `summ` |
---|---|

`PLOT` = string tokens |
What to plot (`cdf` , `histogram` , `ncdf` , `nhistogram` ); default `hist` , `nhis` |

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

`ARRANGEMENT` = string token |
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 or texts |
Groupings of the data values, or descriptions of the variates in the pointer |

`NEWDATA` = variates or pointers |
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 a pointer to separate variates, one for each group. The `GROUPS`

parameter can be set to a text to describe the variates. 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.

### See also

Procedure: `MABGCORRECT`

.

Commands for: Calculations and manipulation, Microarray data.

### Example

CAPTION 'QNORMALIZE example',\ 'Expression values from 9 Arabidopis Slides'; STYLE=meta,plain ENQUIRE CHANNEL=-1; EXIST=check; NAME=\ '%GENDIR%/Data/Microarrays/Hyb-PM_MM.gwb' IF check SPLOAD '%GENDIR%/Data/Microarrays/Hyb-PM_MM.gwb' CALCULATE log2PM = log(PM)/Log(2) DELETE [REDEFINE=yes] Atoms,PM,MM " Do normalization on just three slides for speed " SUBSET [Slides.in.!T('hyb1191','hyb1192','hyb1193');SETLEVELS=yes]\ Slides,Probes,log2PM " Quantile Normalization for 1 Channel Microarray Data." QNORMALIZE [PRINT=summary; PLOT=histogram,cdf,nhistogram; METHOD=means;\ ARRANGEMENT=single] DATA=log2PM; GROUPS=Slides; NEWDATA=nPM ELSE CAPTION 'Microarray example datasets have not been installed.' ENDIF