Exact(2)
Analyses of statistical correlation between the datasets were performed using the GWR method as described above.
The volume and surface renderings for the three-dimensional representations (Fig. 3) and the movie (S1) of the datasets were performed by VolumeGraphics based on the aforementioned segmentations.
Similar(58)
Initial analysis of the datasets was performed using the Agilent ChIP Analytics software (version 1.3.1) to average both replicates as previously described [36].
BLASTX-based taxonomic annotation of the datasets was performed to identify the B. fulgida reads.
Normalization of the datasets was performed using an invariant-set approach.
Analysis of the datasets was performed using STATA 12.0 (StataCorp. 2011) and R software (R-package version 2.13).
In the current study, no central pathologic review across the datasets was performed, hence some differences that we observed might potentially be due to misclassification of tumor grades; additional studies in consistent cohorts are needed to further validate the results.
Additional phylogenetic testing of the datasets was performed by maximum likelihood (ML) analysis with the DNAml software of PHYLIP (PHYLIP [Phylogeny Inference Package] Version 3.6; distributed by J. Felsenstein, Department of Genome Sciences, University of Washington, Seattle, WA, USA).
Analyses of incongruence length differences (ILD; [ 29]) among partitions of the dataset were performed using PAUP* 4.0 [ 30].
The calculation of most of these descriptors for each compound of the dataset was performed using online E-Dragon software (version 1.0).
In order to perform higher-resolution numerical modeling, necessary implementations for the dataset are performed.
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