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By selecting threshold values, the related matrix can be transformed into the adjoining matrixes, which directly measure the couple among different loops.
The second weakness is that the selecting threshold is set via several rounds of experiments, which requires adjusting the parameters in different datasets.
It should be noted that although there are more sophisticated algorithms for selecting threshold levels [25], they will still fail in the case of overlapping pixel intensities between classes the result of noisy data and the cause of "speckle".
The threshold values for the proteasome and TAP predictors (Fig. 1) were derived by applying the MHC-pathway model to a large bacterial protein data set and selecting threshold values which correspond to the estimated specificity of the proteasome (33%) and TAP (76%) [25].
In general, there are many parameters (for example selecting threshold) that need to be determined for any semantic space.
Provided that a set of appropriate positive and negative controls is included on the microarray, ROC analysis obviates the inherent problem of arbitrarily selecting threshold levels in microarray experiments.
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In selecting thresholds, we were guided by the principle of balance, attempting to be neither overly liberal nor overly conservative.
With larger counts the discreteness problem in selecting thresholds for the moving average and Shewhart approaches would be lessened.
While EMSA was used here for selecting thresholds, there could be other, less labor-intensive approaches, for example fluorescence correlation spectroscopy (FCS) [ 51].
But, all the normalized hamming distances are below the selected threshold.
Table 7 shows that the hash distance is greater than the selected threshold.
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