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The results from RMA were obtained with a single call of the algorithm in which all of the files were processed together.
But when we split a homogeneous positive control group, the concept of a good separation of species is altered and it changes the way we interpret the graph of rank value versus cLtlf in the first recursive call of the algorithm.
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It is possible to resist the siren call of the algorithms.
The accelerated computation of values of the form μ i, j is obtained by the application of fast matrix multiplication subroutines between sibling recursive calls of the algorithm.
Clusters shown in this table are from the second round of trying to create smaller clusters, while maintaining correct separation of the Aves group (positive control), or the first recursive call of the ASAP algorithm.
Using the presence call of the MAS5 algorithm identified 124 A-S genes, 76 of which had at least two fold difference; using expression level of 50 as threshold identified 172 A-S genes, 146 of which had at least two fold difference (those with two fold differences are marked with "*" in the second column in Additional file 5).
The selection of the data specific hyperprior parameters is called tuning of the algorithm.
The thresholds for the probabilistic reasoning algorithm, see the Priority Assessment of a call Subsection of the Algorithms Section, were determined by generating 22500 realistic calls and determining the priority each call gets by adjusting the threshold.
The probabilistic reasoning algorithms are detailed in the Priority Assessment of a call Subsection of the Algorithms Section.
This reasoning process is explained in more detail in the Priority assessment of a call Subsection of the Algorithms Section.
As mentioned in the Priority Assessment of a call Subsection of the Algorithms Section, the implementation was optimized to cope with the insufficient scalability of the probabilistic reasoning.
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