There are 6400 spots on each microarray, which you can tell by looking at the number of rows in the file within Excel.

The spots are arranged in four grids (or sectors, as they are called in this godlist). This can be determined by looking at the numbers in the column labeled Sector, and seeing that they match the number of distinct regions visible in the image.

There are 40 rows and 40 columns in each sector, which can be determined by looking at the numbers in the columns labeled Sector Row and Sector Column, and seeing that they match the number of rows and columns within each distinct region in the image.

Note that the overall orientation of the microarray is difficult to determine because of the symmetry: there are 2 metarows and 2 metacolumns, and each grid has the same number of rows as columns. Thus, the image could be rotated 90, 180, or 270 degrees, and the image would still have the same basic layout (4 grids, each containing 40 rows and 40 columns). However, we were able to verify that the tiff files were oriented correctly by matching the images with the figures in the paper.

Most microarray manufacturers now set the number of rows to be different from the number of columns, and mark the array on top or bottom so that the orientation is clear. A mark or special set of spots can also be used to help orient the image of the array.

Bioinformatics Genomics MAGIC Tool Genomics GCAT

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