Beckman Coulter CEQ 8000, User Manual

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User’s Guide 271
The
Minimum Relative Peak Height
value can be adjusted to exclude any data
points generated from small “noise” peaks. The relative peak height is calculated in
the color and size range specified in the initial binning parameters window.
The system also generates Phantom Bins at all intervening positions for whole
number nominal sizes not already assigned to a bin. Phantom bins encompass
expected fragment sizes (based on other observed sizes) that may or may not be
present in the data set.
Selecting the
Show Phantom Bins
check box will highlight the area of all
system-generated phantom bins. Phantom bins can be converted to real bins (alleles)
by right clicking on the desired bin location and selecting the
Create Allele
command from the menu displayed. A line will be added to the
Allele List
representing the new bin and should be checked for consistency.
Selecting the
Show Bins
check box will display the bins with each trace seen in the
stacked trace views.
Investigating Points
Position your mouse-pointer over any point in the bin view plot and left-click to make
your selection. The trace for the point will be displayed for visual comparison to other
points.The visual comparison of the two traces will help you to confirm the
assignment of the data point to an already defined bin, or to a new bin of its own.
The system will assign a Name and Bin ID using the naming and ID conventions
selected in the bin analysis parameters window. The ID assigned by the system reflects
the bin number with a decimal point and the number of bases over that of the bins.
For example : ID = 5.2 indicates a fragment with 5 repeats and 2 extra bases. If you
prefer a different allele ID, you can click on the system suggested ID and make
changes. The final classification is up to the user.
Continue selecting points and viewing their traces until you are satisfied with all the
points in the histogram.
The information for a new allele or the modified information of an existing one is
stored in the system to be applied in later studies. The system automatically
recalculates the statistics based on the edited results.
Updating the Locus Tag and Allele List
Once the bin analysis is complete, the system has generated an allele list based on the
information gathered during the analysis. The list is updated, but at this point has not
been saved to the database. The system prompts you for the locus tag to save to the
generated allele list.