In our experience with single-molecule methylation analyses (23, 43), the rate of single CpG errors which can be due to stochastic methylation errors (biological variation) or bisulfite conversion errors (technical variation) is in the order of several (0 5) percent, depending on the analyzed gene and cell type.
If an experience does not live up to the expected reward, you get what is called 'contrast' in cognitive science, or 'reward prediction error' in biological terms".
Thus the source of the unusual pattern experiment error or biological variation– remains unresolved.
To avoid counting PCR error as biological signal, one could accept as 'real' only MOTU that have at least a certain minimal number of members.
Since technical replicates of a single RNA preparation were used, this experiment captured only technical error, and biological replicates will be more variable.
Translation fidelity assures the production of stable and functional proteomes, but it is not an error free biological process as missense, frameshifting and nonsense errors can all interfere with mRNA translation accuracy [1] [3].
The mismatch rate was 0.5% suggesting that lacking HWE for +1444 may be due to random residual genotyping error, but biological selection bias or other populational inhomogeneity cannot fully be excluded.
For example, Thomas et al. [36] found no evidence of a correlation between body size and substitution rate in invertebrates; such negative results may, in fact, reflect rate estimation error obscuring biological signal in the data.
In addition to the technical error, the biological variability, i.e., the culture-to-culture differences of replicated Synechocystis experiments, was considered using the 3PGA measurement as a test case.
The mean standard error over biological replicates was 0.14 (1.84% relative to the mean).
