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It is also possible that the identification of this site represents a false positive from this analysis.
We interpret these data as evidence that combining both methods provides at least as much resolving power as that of Figure 3. 10.7554/eLife.05949.020 Author response image 2. Dump tetramer and two-color analysis excludes the bulk of false positives from the analysis.
False positives from HRM analysis may be due to the presence of some non-specific amplification, or differences in PCR amplification between samples.
False positives from Mutation Surveyor® analysis can be controlled to a low level by using highly stringent criteria to identify mutations.
The stringent cutoff is utilized to minimize annotations of false positives from the Blast analysis and singletons are not assigned GO terms.
Our risk based analysis is more effective than the conventional "one variable at a time" subgroup analysis, which is plagued by false negative results from poor statistical power and by false positives from multiple comparisons.
Unfortunately, there can be many false positives from this 1st pass in the detector algorithm such that many candidates never pass the threshold for gaining HRI analysis.
Those mentions are likely false positives from BANNER.
All three fragments had some false positives in HRM analysis, ranging from 2.8% to 7.1%.
We incorporated three major improvements to the yeast probabilistic gene network, beyond inclusion of additional data sets: the reduction of bias in the reference training set, the introduction of probabilistic scores for physical and genetic interactions, and the introduction of filters to remove false-positive linkages from analysis of mRNA co-expression.
P-values (false positive rate) from this analysis were then converted to q-values (false discovery rate) using the methodology of Storey and Tibshirani [ 11] as implemented in the Bioconductor q-value routine [ 24].
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