Addressing Microarrays in MAGICTool

Three orientation questions in the Addressing window determine the order in which spots can be numbered on the microarray:

1. Horizontal orientation (spots numbered Left to Right or Right to Left)
2. Vertical orientation (spots numbered Top to Bottom or Bottom to Top)
3. The relative locations of spot #2 and spot #2

It is vitally important to know the order in which spots are represented in the gene list, so they can be numbered the same way in the program. If these questions are not answered correctly, gene names will be associated with the wrong spots, causing all further data analysis to be incorrect.

The following examples show how a grid with 7 rows and 3 columns can be numbered in eight different ways, corresponding to the eight ways the orientation questions can be answered. The headings indicate how the three orientation questions should be answered to achieve each numbering. Here, the numbers 1-21 represent the first 21 genes in the gene list.

Horizontally LEFT to RIGHT
Vertically TOP to BOTTOM		Vertically BOTTOM to TOP
Spot 2 Horiz of Spot 1	Spot 2 Vertical of Spot 1	Spot 2 Horiz of Spot 1	Spot 2 Vertical of Spot 1
Horizontally RIGHT to LEFT
Vertically TOP to BOTTOM		Vertically BOTTOM to TOP
Spot 2 Horiz of Spot 1	Spot 2 Vertical of Spot 1	Spot 2 Horiz of Spot 1	Spot 2 Vertical of Spot 1