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Cluster analysis was made for genes yielding a signal in at least 90% of the samples.
The cluster analysis was made as described previously (Cauli et al. 2000; Helmstaedter et al. 2009): Euclidean distances, Ward's method (Ward 1963), and Thorndike procedure (Thorndike 1953) for linkage distance cutoff (see Fig. 7 B, lower panel), rejecting 1-item clusters (all in Matlab).
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Clustering analysis was made using the same name module in a Partek Genomics Suite Software.
In most cases, the cluster-joining analysis was made with Euclidian distance and complete linkages as the amalgamation rule, that is, distances between clusters were determined by the greatest distance between any two objects in the different clusters.
The switch from DOB-based analysis to date of conception-based analysis was made after many clusters by DOB were found not to be clustered when considered by estimated date of conception, particularly for anomalies where terminations of pregnancy are frequent.
Subsequently, a functional category analysis was made within the six clusters.
Visualization of cluster analysis output was made using ArcMap™ version 10.0 (ESRI Inc., Redlands, CA, USA).
A hierarchical agglomerative cluster analysis was used to create distinct cluster profiles among the FAM measures and discriminant analysis was used to interpret clusters.
Cluster analysis was performed by hierarchical clustering using the Spearman correlation similarity measurement and an average linkage algorithm.
Cluster analysis was undertaken using the BRB gene cluster analysis tool (complete linkage and centred correlation).
Cluster analysis was performed using average-linkage hierarchical cluster analysis with a correlation metric.
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