Additionally, we note that the focal genomic segments with high LogRatios above noise thresholds within each chromosome were repeatedly observed across multiple unique normal sample pair comparisons in both the AA and TCGA CRC datasets, providing further evidence of their being indicative of germline CNVs as opposed to random inherent noise.
This tool leverages the depth of coverage from multiple samples, and from paired samples (e.g. normal/tumor pairs) to identify copy number variable regions.
Nonparametric (Wilcoxon signed-rank or Mann–Whitney test for two samples and Friedman or Kruskal Wallis with Dunn's multiple comparison test for multiple samples) and parametric (paired or unpaired t test for two samples or RM one-way ANOVA or ordinary one-way ANOVA with Tukey's multiple comparison test for multiple samples) tests were performed as appropriate.
In fact, it takes advantage of the extra information contained in paired-end reads and in multiple sample RNA-Seq datasets (e.g., correlation among the samples).
In order to further stratify mechanisms in those that are unique to a pair of samples or common to multiple samples, Information-Theory Similarity (ITS) is utilized to formally assess similarity cross sample pairs versus uniqueness to a pair.
IBD segments from multiple runs for a sample pair are combined by taking the union of the IBD segments from the multiple runs and merging overlapping IBD segments in the union.
Statistical analysis was done using one tailed students t-test for pair wise comparison or ANOVA followed by post-hoc Tukey test for multiple sample comparisons.
Here, sample pairs consist of similar pairs and dissimilar pairs.
For initial evaluation of the VZV avidity assay for CSF samples, three sample pairs of serum and CSF were tested, two from patients with VZV encephalitis (V2.1 and V9.2) and one from a patient with multiple sclerosis (M22).
Only a subgroup of patients underwent multiple samplings, thus paired plasma samples were available for 25 patients at d1 and at d15, for 24 patients at d57, for 21 patients at d155 and for 16 patients at the time of PD.
