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In this case, some genes not in (false positives) are eventually reported by Algorithm 1RMG.
For the mutation data from multiple cancer types, Algorithm 2 GreedyWeight always reports the set of maximum weight; for the mutation data from the gliblastoma study, the set of maximum weight is reported by Algorithm 2 GreedyWeight in 58% of the runs.
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The abundant matched b- and y- ions, accurate precursor ion mass, and expected mass difference from the SILAC pair observed in the spectrum correlated well with the low expectation value or p-value reported by algorithms.
To evaluate the accuracy of the results reported by our algorithm, we compared the steady states that we found to the steady states that are reported in the literature.
The annotations resulting from these hits were reported by the algorithm.
If a model is expressed but not reported by the algorithm, we call it a false negative.
References [ 15, 17- 20, 23] do not discuss the statistics reported by the algorithm, and we are not aware of any reference to what statistics they propose to report.
The manual of the ADMIXTURE code proposes choosing model complexity that minimizes the prediction error on held-out data estimated using the mean deviance residuals reported by the algorithm (K c v ∗ ).
To understand the biological significance of the novel genes reported by our algorithm, we also used the candidate gene prioritization feature of ToppGene [ 32] using the cutoff of P-value = 0.01 with Bonferroni correction.
Note that contigs that fail to align to the reference are still reported by the algorithm, and the variants within them can be explored for variants of functional significance.
First, only limited and prejudiced TRPs were reported by these algorithms because of the algorithm-defined confidence score (16).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com