Changing fingerprint type settings

Question: 

I already have a number of gels stored in my database, and wish to improve the settings for the fingerprint type. Which settings can I safely change and which not?

Answer: 

Settings like image strip and curve Thickness and Nodes can be changed for each gel individually, especially when the scanning resolution or shape differs from gel to gel. Changing the (2-D) Background subtraction and Spot removal has a particular influence on the visual appearance of the gel strips in comparison images, which is not desirable for publication purposes. Settings like band search parameters can be safely changed, as long as the real bands are found more accurately than before, thus saving you editing work. The Tone curve is something which should be adjusted for each gel individually. Image Background color and Foreground color is the only setting that will apply to all gels in the database (also processed gels) and has no other influence. All the other settings will have more or less impact on the compatibility.

  • Curve Background subtraction strength can can be changed safely when band-based comparison is done, when it improves the automatic band searching. When the correlation coefficient is used, large changes may affect the compatibility between old and new gels.
  • The Filtering parameters, especially the Least square filtering can affect the compatibility when correlation-based comparison is used. The parameter has no influence on band-based comparisons, as long as real bands on the patterns are defined correctly.
  • Changing the Reference system has the most dramatic influence on the compatibility between old and new gels. Adding or deleting reference positions will cause a new reference system to be created in the fingerprint type. Previous gels, with the first reference system, and new gels, with the new reference system will be remapped based upon the molecular weight regression curves of both reference systems. Since regression into molecular sizes causes error, this situation is to be avoided whenever possible. Only changing the relative positions of the reference positions on the other hand will create a new reference system which is compatible with the previous through a non-linear transformation between both reference systems. This transformation causes almost no error, and allows users to switch to redefine their reference positions based upon a better pattern, e.g. from a gel run under better conditions. It also allows different sites to compare gels without loss of quality, as long as the sites use the same set of markers in their reference systems.

Package(s):

Applicable for: 
Version 1.0 - 7.6

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