Download PathwaysTM 4 Software User's Guide

The synthetic microarray view is not available if the framework being used does not
supply geometry (X and Y coordinates).
The coloring on synthetic views depends on painters selected from the toolbar.
For microarray(s) or condition(s), the synthetic array shows expression levels. Three
painters are available.
1 Color: highest normalized intensity is bright red, lowest is dim blue
2 White on black: highest normalized intensity is white, lowest is black
3 Black on white: highest normalized intensity is black, lowest is white.
For microarray pair(s) or condition pair(s), the synthetic array shows upregulation or
downregulation. Two painters are available.
1 Ratio: upregulation (high ratio) is green, downregulation (low ratio) is red,
brightness is relative to the normalized intensity of contributing spots
2 Difference: upregulation (high difference) is red, downregulation (low difference)
is blue, brightness is relative to the normalized intensity of contributing spots
A Brightness slider increases spot brightness. Moving the slider to the right allows viewing
low intensity spots.
The synthetic microarray may also display invalid clones. Once a microarray is added to a project, individual spots can be marked as invalid by right-clicking on the detailed view of a selected clone and selecting the Invalid clone option.
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