Download AIDA Microarray for Windows User's Manual

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Setting Parameters
In some cases, you might want to adjust the default parameter settings for the alignment
and/or calculation process. You can do this using the Settings panel of the Array
Definition toolbox. Choose the parameter set you want to change from the Settings dropdown list.
Alignment Settings
If you choose the Alignment menu item, the appearance of the lower part of the toolbox
changes, revealing control for setting alignment parameters.
Figure 3-49
Alignment Controls
With the Alignment controls you can set default parameter values for the automated
alignment processes used to match the position of the defined array spots with the real
position of the dots in the array. This alignment process is consequently accomplished by
the integration of the intensity values of each spot.
The alignment process can be varied by the following parameters:
• Local Positioning: Adjusts the position of the array to the image locally.
• Segmentation: Choose Fixed Diameter to enter a fixed diameter value for all dots
or choose Adapted Diameter to let AIDA determine the diameter of each dot
automatically. If you choose Adapted Diameter, you must specify the allowed
diameter variation range using the Dia. max/Dia. min spin boxes.
Performing Microarray Evaluations
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