The CK model is the most accurate of the methods evaluated here, but too time consuming for engineering applications, although recent developments may partly overcome this shortcoming.
Most of the eight unsupervised methods evaluated here can be tuned by selection of parameter values.
The surveillance methods evaluated here are primarily useful for detecting outbreaks caused by resistant organisms.
Of the other alignment-free methods evaluated here only CVTree showed a consistent improvement over the baseline.
The choice of priors in the analysis of non-linear methods evaluated here, did not significantly affect reliabilities.
As also shown in Table 2, there was no overall significant difference (p-value: 0.266) in the rate of contamination between the four decontamination methods evaluated here.
Furthermore, the values of diagnostic parameters, including specificity, sensitivity, positive and negative predictive values and positive likelihood ratio, are the highest among the three methods evaluated here.
In summary, the cytokine measurement methods evaluated here were found to be reproducible for laboratories using commercial assay platforms; however, the measured values of identical samples varied across laboratories and assay platforms.
The similarity score between a gene and a pathway was calculated by the annotated GO terms of the gene and the overrepresented GO terms of the pathway using the 6 methods evaluated here.
The five methods evaluated here are: MAS 5.0 (Affymetrix Inc., 2002), RMA (Irizarry et al., 2003), GCRMA (Wu et al., 2004), FARMS (Hochreiter et al., 2006) and DFW (Chen et al., 2007).
