Does a robust means analysis for Affymetrix slides (D.B. Baird).

### Options

`TRANSFORMATION` = string token |
How to transform the data (`log2` , `none` ); default `none` |
---|---|

`MAXCYCLE` = scalar |
Maximum number of iterations; default 50 |

`TOLERANCE` = scalar |
Tolerance for convergence; default 0.0001 |

### Parameters

`DATA` = variates or pointers |
Expression data to be summarized |
---|---|

`SLIDES` = factors or texts |
Defines the slides |

`PROBES` = factors |
Defines the probes |

`IDPROBES` = factors |
Saves the probe IDs |

`MEDIANS` = variates or pointers |
Saves the robust means |

`SEM` = variates or pointers |
Saves approximate standard errors of the robust means |

### Description

`MAROBUSTMEANS`

calculates the medians of probe expression values across a series of Affymetrix slides. The median expression level for each slide is estimated and removed in a iterative fashion using an algorithm called the median polish algorithm. An approximate standard error of the mean can be calculated which is defined as 1.483 times the median absolute deviation from the probe medians.

The expression intensity values are supplied by the `DATA`

parameter. If these are in a single variate, the `SLIDE`

parameter should supply a factor to index the slides, and the `PROBES`

parameter should index the probes or genes. Alternatively, you can supply a pointer containing a variate for each slide. The `SLIDES`

parameter can be omitted, or it can supply a text to label the slides in the pointer. The `PROBES`

factor refers to a single slide, and all the slides must have a common layout.

Options: `TRANSFORMATION`

, `MAXCYCLE`

, `TOLERANCE`

.

Parameters: `DATA`

, `SLIDES`

, `PROBES`

, `IDPROBES`

, `MEDIANS`

, `SEM`

.

### See also

Procedures: `AFFYMETRIX`

, `FDRBONFERRONI`

, `FDRMIXTURE`

, `MAANOVA`

, `MABGCORRECT`

, `MAEBAYES`

, `MAREGRESSION`

, `MARMA`

, `MAVDIFFERENCE`

, `MAVOLCANO`

, `QNORMALIZE`

.

Commands for: Microarray data.

### Example

CAPTION 'MAROBUSTMEANS example'; STYLE=meta ENQUIRE CHANNEL=-1; EXIST=check; NAME=\ '%GENDIR%/Data/Microarrays/Hyb-Expressions.gsh' IF check SPLOAD '%GENDIR%/Data/Microarrays/Hyb-Expressions.gsh' " Calculate robust means over Slides and Atoms for each probe." MAROBUSTMEANS [TRANSFORM=none] Expression; SLIDES=Slides; PROBES=Probes;\ IDPROBES = ProbeID; MEDIANS = Exp_Medians; SEM = Exp_SE FSPREADSHEET ProbeID,Exp_Medians,Exp_SE ELSE CAPTION 'Microarray example datasets have not been installed.' ENDIF