Use this to set options in the Calculate Affymetrix Expression Values menu.

## Model fitting

This controls the parameters for the various summary methods that can be selected.

## Maximum number of iteration cycles

For the RMA and RMA2 analyses, the summary over probes uses a median polish algorithm. This sets the maximum number of iteration cycles when removing the medians over atoms and slides.

## Tolerance for convergence

For the RMA and RMA2 analyses, the summary over probes uses a median polish algorithm. This sets the convergence tolerance for this algorithm, so that when the results changes by less than the specified amount, the algorithm is deemed to have converged.

## Background correct intensities

For all algorithms, the lowest 2% of spots on each slide can be used to estimate a background correction for the intensities. The chip is divided into 16 zones in a 4 x 4 grid, and each spot has a weighted average of these 16 levels removed from it. The levels and the weighting used are controlled by the next two options:

### Using 2%

This controls the how the background levels are estimated:

Means |
The means of the values below the 2% quantile are used as the background levels |

Quantiles |
The actual 2% quantiles are used as the background levels |

### Weighting

This controls the how the background levels are combined before removing them from each spot:

Affymetrix |
The weights are 1/(squared distance + 100) |

Distance |
The weights are 1/(min(squared distance,100) |

Where squared distance is the (distance from the spot to the zone centroid)**2.

### Normalize intensities

Performs a quantile normalization of the PM/MM values on each slide using the same method as in the One channel Quantile Normalization menu. The method of summarizing over the slides is controlled by the next option.

### Summarize using

Specifies which way that the overall distribution is produced from the CDFs from each slide.

Means |
The mean is taken across CDFs. |

Medians |
The median is taken across CDFs. |

Geometric means |
The geometric mean is taken across CDFs. This is the mean on the log scale, back-transformed to the natural scale. |

## Display

The results to be displayed in the Output window:

Parameters |
The parameters fitted in the RMA/RMA2 models. |

Background levels |
The background levels in each of the 16 zones used for background correct of Affymetrix slides. |

Monitoring information |
Progress details on the analysis completed so far. |

## Action buttons

OK |
Store the options and close the dialog. |

Cancel |
Close the dialog without making any changes. |

Defaults |
Reset options to their default settings. |

## Action Icons

Clear |
Clear all fields and list boxes. | |

Help |
Open the Help topic for this dialog. |