Define the basic geometry of a batch of microarray images

Description

`SetParameters' is an interactive function for specifying the basic geometric structure of a set of microarray images. The array dimensions can be specified by the arrangement of grids (e.g. 4x4) and the arrangements of spots within grids (e.g. 19 x21).

Usage

SetParameters(batch)

Details

The user is prompted for values for the following parameters:

The last two of these parameters correspond to the amount of positional variation expected between images in the batch. See the Spot user's guide http://www.cmis.csiro.au/iap/Spot/spotmanual.htm

Value

None.
A file named "parameters.<batch>" containing the specified information is created in the current directory.

Author(s)

Jean Yang

References

Spot user's guide. http://www.cmis.csiro.au/iap/Spot/spotmanual.htm

See Also

SetTemplate, Spots, SpotRGB

Examples

> SetParameters("array1")
Enter number of rows of grids per image (ngrid.r): 4
Enter number of columns of grids per image (ngrid.c): 4
Enter number of rows of spots per grid (nspot.r): 19
Enter number of columns of spots per grid (nspot.c): 21
Enter top/bottom translation tolerance, default is 50 (tolerance.r): 20
Enter left/right translation, default is 50 (tolerance.c): 30
Initialization complete