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CN call thresholds were defined: high gain +0.7, gain +0.3, loss −0.3 and homozygous loss −0.7.
These 26 mutations were re-examined with Mutation Surveyor®, and the mutation call thresholds were set to accept the mutation when the mutation height is near or above 500 and the background noise in surrounding base pairs is zero.
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The idea is to overcome what Taubman likes to call "threshold resistance," which is the physical and psychological barrier that stands between a shopper and the inside of a store.
All individuals were successfully genotyped at call rate >98.1% with genotype call threshold of 0.15.
It suggests that a higher P/A call threshold might be more appropriate in routine Affymetrix expression array data analyses.
As shown by genotypes calls in leukemia cohort, ALG is highly accurate, provides a very low no call threshold and performs very well when compare to commercial software.
The higher specificity value achieved by Dindel is likely due to the minimum variant call threshold used in analysis.
Genotype calls are made using genotype posterior probabilities [using the π i inferred from this step unlike (2.3)] with a 0.7 call threshold.
If the function was non-linear, we selected a temperature breakpoint (which we commonly call "threshold") by minimizing the Akaike Information Criterion (AIC) for a range of different threshold values.
Consequently, it is no longer necessary to consider the base pairs whose pairing probabilities are at most the thresholds θ(p ), which we call threshold cut.
The default set cluster file was HumanOmni2-5 M-8b1-1_B.egt (Illumina), and a Gen Call Threshold of 0.15 was used for SNP calling.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com