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Two SNPs were excluded because their genotypes were automatically defined by the call algorithm in ≤ 90% of the adequate samples.
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We defined genotype-call error as the proportion of genotypes that were assigned an incorrect genotype by the calling algorithm.
All the three qPCR experiments resulted in a deletion for the oldest twin, and a CN of 2 for the youngest, confirming that this is indeed one large deletion that was artificially split by the calling algorithms.
As mentioned above, this can be accomplished by increasing the stringency settings of the calling algorithm [18].
In some cases, the signal change was detected by a single BAC clone but not in genomically neighboring clones, and was therefore ignored by the CGH calling algorithm.
When both template and complement strands are sequenced these are combined by the base-calling algorithm to produce 2D reads, which may be divided into two types.
Considering the absolute gene expression status, we further found that probes identified by the paired t-test in controls had a larger proportion of noninformative probes (60.5%) that had absent calls assigned by the Detection Calls algorithm in every tested array compared with those in welders (47.3%).
In principle, reporting the probabilities of all four bases would provide downstream analyses with the complete information derived by the base-calling algorithms.
For the deletion in chromosome 19, a heterozygous deletion was confirmed in five cases and one control with an additional case deletion detected that was called copy normal by the CNV calling algorithms.
The oNCS nurse call algorithm is implemented by using Rules.
We are primarily interested in the running time of Algorithm 1, for which the time per iteration is dominated by the cost of calling Algorithm 2, which in turn is dominated by the cost of the algorithm used to find directed MSTs.
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