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Thus, not only can K a / K s detect drug resistance mutations in a single dataset (with no requirement for a reference dataset of untreated samples), it can do so even when the primary dataset is contaminated with a large fraction of untreated samples, or samples with different treatments.
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These nine datasets were contaminated with 0 100% noise in the form of simulated reads from Proteobacteria genomes.
It is not a surprise to observe negative biases when the simulation datasets were contaminated, because flipping the outcomes of the records that have the very low or very high probabilities tend to weaken the associations between the exposure and the outcome leading the associations towards null.
For each of the 24 scenarios, the simulation datasets were contaminated by flipping the outcomes (Y becomes 1- Y) of the records that had the extreme probabilities of having Y = 1 (i.e., either very low or very high p y ).
Nothing is contaminated.
"The water is contaminated, very contaminated.
Water is contaminated.
The drinking water is contaminated.
How much chicken is contaminated?
The food supply is contaminated.
Most of it is contaminated.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com