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Many recent articles use similar strategies to target specifically time-lapse light microscopy datasets (Delpiano et al., 2011; Lombardot et al., 2008; Pizarro et al., 2011), which demonstrate the general interest in applying optical flow to the type of datasets presented in this article.
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Selection of the sequence and its organism is determined based on the type of dataset to be analyzed.
The type of dataset itself also can impact the rate of malignancy found in a given population.
Predefining and constraining the types of datasets helps to maintain the integrity of the datasets used.
Of all the types of datasets in our analysis, expression data is the most abundant.
The averages of ERR (relative to the CMN) across the types of dataset for the '6 NNs' and '12 NNs' configuration were 41.7% and 41.1%.
Generate 100 reference sample datasets from random number generators with distributions defined by the fitted functions used in step 2. Re-fit each of these 100 reference sample datasets to the type of distribution from which they were drawn in step 3, and estimate the test statistic for simulated data, ds.
Finally, since EUCALYPT can be applied to any type of datasets compatible with the model, we also tested it on a genes-species dataset from [ 17] that had previously been used by [ 20].
To validate the type of effects observed when pooling artificial datasets, we applied the same analysis to a compendium of six breast cancer datasets (Desmedt et al. [ 4], Minn et al. [ 22], Miller et al. [ 18], Pawitan et al. [ 23], Loi et al. [ 24], Chin et al. [ 25]).
In order to identify compositional elements that are potentially involved in effecting inactivation (or escape), the program TEIRESIAS [14] was used to identify patterns in the DNA sequences that are unique to one type of dataset (the input sequence used was masked for low complexity repeats).
We used the CPT codes [ 15] in the claims dataset to identify the type of surgery performed.
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