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For simplicity, hierarchical clustering was used to examine sample relationships.
A popular approach for exploring sample relationships is cluster analysis.
The advantages of using network methods for describing sample relationships in genomic datasets are summarized below.
Principal component analysis (PCA) using all transcripts was performed for visualization of sample relationships.
Thresholding improves sample clustering (see below), provides a read-out for sample annotation, and simplifies quantification of sample relationships.
Sample relationships were examined using principal components analyses that revealed no strong technical effects, which may encumber the subsequent analyses.
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Besides, manifold learning algorithms not only reduce the feature dimensions but also preserve the sample relationship of the same classes under various illumination conditions.
The sample relationship in the SqCC subtype data is shown in the MDS plot.
Hierarchical clustering and principal component analysis was performed on the normalized signal data to assess the sample relationship and variability.
In this sample, relationship style prevalence, based on attachment theory, is similar to that in found in the general population [ 30] and in another medical school sample [ 20].
We checked the sample relationship in the SqCC-subtype gene-expression data and the four subtypes were roughly clustered by themselves.
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