Flags are attributes that denote the quality of the entities. Using these attribute values in GeneSpring we filter the genes.
These values are generated based on the feature quality on the chip, like signal saturation and signal uniformity.
The genes which are given low significant attribute in the data file would be marked as 'Absent' and high significant values would be marked as 'Present'.
These flags are generally specific to the technology or the array type used. Thus the experiment technology type, i.e., Agilent Single Color, Agilent Two color, Affymetrix Expression, Affymetrix Exon Expression, and Illumina Bead technology determine the flag notation.