microarraysscreening

GAL file format

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: