Microarray Calculate Affymetrix Expression Values Options

Model Fitting

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

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

Perfoms 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 CDF's.
Medians	The median is taken across CDF's.
Geometric Means	The geometric mean is taken across CDF's. 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 the options to their default settings.