The Filter by Flags functionality for Affymetrix data could be used when you are working with .CHP files. The CHP files contain the flag information.
If you are working with .CEL files then use MAS 5.0 summarization to generate the Flags.
The Filter by Flags functionality for Affymetrix data could be used when you are working with .CHP files. The CHP files contain the flag information.
If you are working with .CEL files then use MAS 5.0 summarization to generate the Flags.