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Masks are rarely used features in MAS. There are three types of mask files:
Image mask files: You may want to use an image mask if there is a large visible aberration on an image. You define the image mask based on the physical location of the image. Probe pairs included in the mask are excluded from the analysis. Image masks are associated with a given .dat/.cel file and cannot be used on other images.
Probe mask files: Probe masks are defined by the probe set and probe pair number. Probe pairs included in this type of probe mask are excluded from the analysis when the probe mask is used. Probe masks can be applied across a data set. For a detailed description, please refer to Affymetrix Microarray Suite User's Guide (P/N 701099).
A second type of probe mask defines a select group of probe sets that can be used in normalization or scaling. Please refer to Affymetrix Microarray Suite User's Guide where this type of probe set mask file is described. |