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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.
These data were then automatically tabulated in a tab delimited file to generate a matrix of gene expression patterns across all spatial domains.
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.
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.
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.
A matrix of expression slice is constructed according to the matrix of gene expression dataset.
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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.
Further, to obtain a matrix of gene-level expression values we used the exprs function with parameters by default.
The resulting data were converted into binary matrix of gene-miRNA interactions between 18440 genes and 779 miRNAs.
B is a p × p matrix of gene-to-gene causal effects, where the element β i j represents the partial regression coefficient of the regression of gene i on gene j.
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