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We can call the assumption corresponding to this the equal probability assumption.
One might argue that one has no more reason to suppose that the equal probability assumption is true than the equal quality assumption.
Therefore, in judging the evidence, a key issue is which of the two assumptions, the equal quality assumption of Figure 1 or the equal probability assumption of Figure 2 is more relevant (there is still, of course, the issue of the identical distribution assumption, to be discussed below).
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The inconsistency between the conclusions obtained under the two pooling probabilities assumptions is the result of the fact that isoform-specific peptides associated with AS events have higher pooling probabilities under the " equal pooling probability" assumption than under the " equal expression" assumption.
Under the first assumption to which we refer as the "equal pooling probability" assumption, all in silico generated peptides are equally abundant and therefore have the same probability (1/N) of being pooled, which depends on the size of initial peptide population (N).
The first, " equal pooling probability" assumption, indicated that AS events were under-represented in all experimental peptide sets.
The first assumption, to which we refer as the " equal pooling probability" assumption, has previously been described by Tress and co-workers [ 12].
This difference results in different pooling probabilities, in which the " equal pooling probability" assumption provides an upper bound to the expected number of AS events.
Advantage of Mth models applied to cancer datasets, is the ability to explore individual factors associated with capture heterogeneity, as equal capture probability assumption is unlikely.
In a previous proteomics study performed on Drosophila data, the same " equal pooling probability" assumption was used for generating peptide samples and determining the number of expected AS events [ 12].
Under the " equal pooling probability" assumption, the number of experimentally confirmed AS events in the Castellana set was 2.2 times smaller than the expected number of events as determined by the in silico experiments (Table 4; Simulations A).
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