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RaceID first identifies large clusters defined through k-means clustering of the expression correlation matrix of genes.
A phylogeny of the isolates was also constructed using Dollo parsimony based on the presence and absence matrix of genes [50] implemented in PAUP4.0b10.
DSPR no covariance raw residual matrix of genes in the sex hierarchy GRN.
CEGS no covariance raw residual matrix of genes in the sex hierarchy GRN.
These lists are summarized in a large matrix of genes and topologies, which is subsequently treated by clustering methods.
This tabular matrix of genes × samples usually contains a large number of genes (i.e. large p features) but a much smaller number of samples (i.e. small n samples).
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First we consider a new scheme of visualizing variation in substitution rates amongst genes and lineages which uses a matrix of gene tree branch lengths.
The matrix of gene expression was then transformed to presence/absence because of the uncertainty involved in the copy number calculation due to the amplification step.
PCA applies a singular value decomposition to the covariance matrix of gene expression data to identify the combination of conditions that explain the greatest variation in the data.
These data were then automatically tabulated in a tab delimited file to generate a matrix of gene expression patterns across all spatial domains.
We assembled a matrix of gene family sizes for: Canis familiaris (dog), Rattus norvegicus (rat), Mus musculus (mouse), Pan troglodytes (chimp), and Homo sapiens (human), for analysis of mammalian gene family evolution.
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