First, because genetic variations and some network properties varied among the simulation replicates for the same parameter set values, we examined the effects of varying values of these properties.
Biological replicates for the same cells or tissue are also more similar to each other than to distinct cell or tissue types, indicating that differences in MAE related to lineage are more important than those caused by inter-individual or technical variability.
The same comparison is replicated for the control group.
Replicated samples for the same patient were averaged.
If different replicates for the same subject belong to different classes (such as measurements taken at different time points), only replicate-level classification is produced.
The mixed effect model accounted for potential correlation in signal intensities that may arise from having multiple brain regions from the same subject as well as having multiple technical replicates for the same brain regions.
Expression levels within biological replicates for the same tissue were highly correlated (mean: 98.3%, range 97.1%-99.6%%).
An average fluorescence ratio (Kf) value of replicates for the same sample was determined and the standard deviation (S.D).
It is noteworthy that expression between qRT-PCR replicates for the same individual at each stage (technical replicates) were highly consistent, whereas the levels between different individuals (3 biological replicates) varied, resulting in relatively high standard deviations.
For the subject displayed, the variability associated with extract replicates is larger for the 1.5K panel in comparison to the 24K panel; the standard deviation associated with the difference in expression between extract replicates for the same tumor sample is 0.69 for the 1.5K panel and 0.214 for the 24K panel.
