GenePix Array List (GAL) files are text files with specific information about the location, size, and name of each DNA spot on a microarray. They are therefor of vital importance for the analysis of scanned microarray images. The format defines a specific header before the list of data columns follows:
Example:
ATF 1 9 5 Type=GenePix ArrayList V1.0 BlockCount=1 BlockType=0 "Block1=10000, 38780, 150, 20, 200, 18, 200" Supplier=BioRobotics ArrayerSoftwareName=TAS Application Suite (MicroGrid II) ArrayerSoftwareVersion=2.7.1.18 ScanResolution=10 Block Column Row ID Name 1 1 1 RP11-163J21 Clone 1 1 1 2 RP11-163J21 Clone 2
Explanantions:
ATF -> File conforms to Axon Text File
1 -> Version number of ATF
9 -> Number of header lines before the “Block, Column, Row, …” line
5 -> Number of data columns (Block, Column, Row, Name, ID)
Type=GenePix ArrayList V1.0 -> Type of file, same for all GAL files
Block Count=1 -> Number of blocks described in the file
Block Type=0 -> Type of block, 0 = rectangular Block
X=A, B, C, D, E, F, G -> The position and dimensions of each block.
A -> xOrigin
B -> yOrigin
C -> Feature diameter
D -> xFeatures
E -> xSpacing
F -> yFeatures
G -> ySpacing ScanResolution – Optional parameter to scale the position on higher-resolution images Block arrangement
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
The data columns are:
- Block
- Column
- Row
- Name
- ID
Further reading and sources:
