Feature masking is when a user identifies features in the GCOS image display window and clicks the  "mask" button. The list of X/Y coordinates of those "masked" features are stored within the CEL file.

The purpose of masking is to allow a user to identify features to exclude from subsequent analyses. The MAS5 expression analysis algorithm, implemented in the GCOS software, was designed to exclude features that have been "masked" from its analysis. The MAS5 algorithm will mask out both probes of a probe pair when one has been masked.

Probe pair masking is when a user defines one or more probe pairs from a probe set to exclude from an analysis. The MAS5 expression analysis algorithm, implemented in the GCOS software, was designed to exclude features that have been "masked" from its analysis.

The list of probe pairs to exclude from an analysis is stored in a MSK file. The GCOS software prompts the user for the probe pairs (one based indexing) and stores them in a MSK file as zero based indices. File format documentation and file parsing software developers kits are available for the MSK file.

The difference between feature masking and probe pair masking is that feature masking is performed due to defects on an individual array whereas probe pair masking is performed due to probe pairs that have been determined to not perform to your specifications.

Unlike the masked section in a CEL file, a user can create multiple MSK files for a given array type where each MSK file was created based on different requirements or specifications.

When developing algorithms that analyze intensity data from CEL files, consider using the MSK file and masked section in the CEL file as a method to allow a user to selectively exclude probes and probe pairs from the analysis.