Vocabulary


Addressing is the short process of telling MAGIC Tool the layout of the spots and grids in the tiff file as viewed within MAGIC.

Chip is a synonym for a microarray.

Feature is a synonym for a single spot on a microarray.

Flag is a verb that means you mark a particular spot to indicate its data are not reliable. This may be due to high background in the area, a dust bunny sitting on the spot, etc.

Grid is a compact arrangement of spots with even spacing.

Gridding is the process that MAGIC uses to find the spots on your tiff files

Metagrid is a higher order level of organization. A set of grids are organized into groups called metagrids. For a more complete description, see this web page <www.bio.davidson.edu/projects/GCAT/Griding.html>.

Segmentation is the process of finding the signal and distinguishing it from the background. There are three methods in MAGIC. Fixed circle is the fastest, and recommended for most purposes.  Adaptive circle and seeded region growing are also provided. 

Tiff files (e.g. file_name.tif) are the raw image data that are produced when a DNA microarray is scanned. One tiff file is produced for each color on each chip.