On the Analysis of Optical Mapping Data - University of Wisconsin ...

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statistical techniques may also be used. Naturally, not all cuts present are always detected,
nor are all reported cuts real.
Lengths: Once cut sites are identified, the intensity profile between cuts is integrated to
obtain a total intensity of the corresponding restriction fragment. These measurements then
need to be scaled appropriately to convert them to base pair units. Due to variability in
experimental conditions, the scale factor is usually different in different surfaces and channels,
and possibly even within a channel. To deal with this, DNA molecules with known length
and restriction pattern, called standards, are placed in the sample along with the DNA
being mapped. These standards are identified in the images based only on their pattern.
Their measured fluorescent lengths and known base-pair lengths are then used to scale other
fragments. Naturally, the measured intensities of the standards are themselves subject to
noise, and the scale is usually estimated as a smooth function of position on the image.
Figure 1.4 shows the distribution of standards on a typical surface along with the estimated
scale.
Quality: A critical theme in the optical mapping system is the automated processing of
massive amounts of data, beginning with image processing. Only a fraction of the fluorescent
material seen in raw images is ever marked up by the image processing step and reported as
optical maps. This filtering is important to ensure a certain minimal quality in the optical
map data one works with. Of course, the automated processing is not perfect and certain
maps are marked up wrongly; subsequent methods need to be able to deal robustly with
these errors. Most existing methods treat all maps equally once they are reported by the
image processing software. However, it is likely that some weight or measure of confidence
reported along with every map would be useful in further analysis. This is an area that could
benefit from further research.