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Their recommendation was based on the Mutual Coverage criterion they defined to measure the extent to which gene sets deemed significant by one method are reproduced by other methods analysed by the authors, based on a collection of >100 experimental data sets.
Furthermore, some TF pairs considered as false positives by one method are considered bona fide cooperative TF pairs in other, for instance YNL216W (Rap1) – YIR018W (Yap5), considered as a potential false positive pair by method C (due to lack of experimental support) and accepted by method N as a part of the same cooperative module.
Note that more than 70% of all positions predicted by one method are also identified by other one or two methods.
The adjusted Rand coefficient quantifies the global agreement between two methods, whereas the Wallace coefficient indicates the probability that two isolates classified as the same type by one method are also classified as the same type by another method [13].
The W coefficient provides a finer comparison between two typing methods, since the value indicates the probability that two strains classified as the same type by one method are also classified as the same type by the other method.
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In a few cases, a risk identified by one method was divided into more than one risk by the other.
Second, we test whether a nucleosome predicted by one method is close to a nucleosome predicted by another.
McNemar's test was used to test whether number of subjects or teeth with DDE detected only by one method was significantly higher than the other method.
DE genes (only protein coding genes were considered) detected by IMM were intersected with DE genes detected by TMM and DE genes only detected by one method were retrieved.
The multivariate model revealed that RHT was strongly associated with standard testing in the past 6 months, indicating that a person tested by one method is likely to also be tested by another method.
Moreover, 58 proteins (20 out of 20 proteins predicted by two methods and 38 out of 504 proteins predicted by one method) were additionally predicted as PP proteins (Additional file 1).
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