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Following the identification of the differentially expressed probesets (corresponding to mRNAs or miRNAs), the corresponding matrix of expression values for all the microarray hybridizations performed were analysed using the hclust clustering algorithm, implemented in R [ 110].
We started with a matrix of expression values (median-centered log-intensity values divided by standard deviation) for the 156 samples (Figure 2A).
The module eigengene, the first principal component of the matrix of expression values of a given module, was adopted to characterize the gene expression profile of the module [23].
ARACNE predicts interactions based on a matrix of expression values and a list of regulators.
Second, we used the pairwise correlation matrix of expression profiles across all arrays for additional QC.
A matrix of expression slice is constructed according to the matrix of gene expression dataset.
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Correlation matrices of expression files reveal the presence of intricate networks of probe expressions.
We examined the matrices of expression again after filtering out 36 human and 12 mouse OR-related probesets, whose specificity or sensitivity was less than 1.
Two-way hierarchical clustering, with results visualized as heatmaps, has served as the method of choice for exploring structure in large matrices of expression data since the advent of microarrays.
A file containing an n x m expression matrix of normalized expression values, where n is the number of probe sets and m is the number of samples, was generated for each cluster.
Calculate the matrix Z of expression levels of all the genes in the HelaS3-ifn α4h comparing to the HelaS3.
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