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Our extensive experimentation with both real and random instances shows that the proposed procedure competes with the best-known algorithms in terms of solution quality, and has reasonable computing-time requirements.
A plot of the above 3 parameters using both real and random data helped to generate the cutoff criteria for analyses of significant linkages (Figure 1 & Figure 2).
The normalized HES for both real and random clusters were aggregated, then sorted in decreasing order.
Additionally, the reliability of the methods was tested by comparing both real and random genomic DNA.
(iii) Then, C (1,1), C (0,0), and C (−1, −1) are calculated for both real and random profile pairs.
We therefore recommend to run BLSSpeller with relaxed parameter settings on both real and random data, and to filter this output using more stringent parameters until a reasonable FDR is obtained.
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An extension of both the real and random distributions for the pS/pT case was added to additional file 5 (for those taking interest in the distribution tail).
The relative low abundance of relatively large proteins in both the real and random interaction data can explain the trends in Figure 5A C.
In order to be able to compare HES across different motifs (which might have different cluster sizes), we normalized all HES (both for real and random clusters) using their mean μ HES and the standard deviation σ HES, calculated over 1000 random clusters.
For each species, the counts of overlapping genes (OGs), overlapping gene pairs (OG pairs), and overlapping gene clusters (OGCs) coming from both real data and random simulations are shown.
For comparison, the closeness of real and "random" EEG normalized histograms is about 0.147.
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both real and perceptual
both real and ideal
both real and nominal
both concentrated and random
both real and fake
both engineered and random
both real and potential
both simplified and random
both systematic and random
both predictable and random
both real and complex
both real and distinct
both simultaneous and random
both real and deep
both clumsy and random
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com