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The efficiency in using the transformed dataset to perform normal/tumor classification was investigated using feature partitioning with informative features (gene annotation) as discriminating axes (single gene expression or pair-wise gene expression ratio).
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The data were log-transformed, arrays and genes were median-centered and the transformed dataset was hierarchically clustered using uncentered correlational clustering.
Therefore, the original dataset contains 5 variables while the transformed dataset contains 20 variables.
The transformed dataset exhibited lower CV when compared to that of single gene expression.
Logic minimization was then applied to generate sets of simple rules to describe the transformed dataset.
To provide an unbiased global view of these genomic profiles, we performed unsupervised hierarchical cluster analysis using the CGHsmooth transformed dataset [ 30].
The transformed datasets were then hierarchically clustered using Cluster 2.11 and the results displayed using Treeview 1.60 [69].
Homogeneous real gene expression data from any experiment can be used to create a transformed dataset with controlled balanced changes introduced into a portion of the genes measured in the array.
Such normalized and transformed dataset was then used for detection of cancer specific methylation profiles, and secondarily to differentiate between PP4 and PP3-specific methylation profiles.
The 24-fold cross-validation (using the log transformed 24 hr kitchen concentration dataset) provided an overall correlation coefficient between modeled and measured values.
Joly and Bruneau [ 33] emphasized the combination of transformed datasets from several loci for phylogenetic analyses.
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