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In most cases, parallelization at the array level is better (it results in smaller users' wall time).
Following the main results with HMM and CBS, wavelet-based smoothing and CGHseg are parallelized at the array level.
In contrast to parallelizing at the array level, parallelizing at the array by chromosome level can use all available CPUs when there are few arrays.
GLAD and PSW are parallelized at the array level as the code of the basic algorithms themselves would not allow for easily maintainable finer grained parallelization.
Figure creation in the web-based application is parallelized at the array level, by writing to a shared directory (accessed via NFS), except for the figures where all arrays are superimposed, where parallel execution is impossible.
For HMM, BioHMM, and CBS we have compared parallelization at the array by chromosome vs. at the array level, and for ACE we have compared parallelization at the array by chromosome vs. at the chromosome level.
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Below we further study the high-scoring co-training matches (both at the dataset and at the array levels) and show how they can be used to derive biological insights about processes and diseases.
Bypassing printing steps, microarrays or even oligo-chips from third party providers can also be loaded into MAF, albeit with less detailed annotation at the array design level.
Also, an anomalously large first component in a singular value decomposition analysis[ 9] pointed to problems at the array batch level.
The availability of a whole-genome assembly of T. castaneum mapped to chromosomes was the most important prerequisite in addressing these issues, making possible examination of TR evolution at the chromosomal and at the repeat-array level.
For the aCGH algorithms considered, there are embarrassingly parallelizable computations at the chromosome by array level.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com