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The biomarkers are the top-ranked features with the largest statistic values or the smallest p-values, i.e. we pick the three top-scored biomarkers for the sake of 3-dimensional visualization convenience.
In this experiment, the parameters of R-SAE are set the same as in Section 3.1 that only the unit number of the output layer is set to 3 for visualization convenience.
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For the convenience of visualization, a rank-2 approximate biplot is considered.
In this manner, raw NuPop scores were converted to plots using in-house shell scripts for convenience of visualization.
For the convenience of visualization, two sets of Cartesian coordinates are set with X- and X'-axes intersecting the axes of Hole #1 and Hole #2, respectively.
For convenience of data visualization, raw area counts for each biochemical were re-scaled by dividing the value for a specific biochemical in each sample by the median value for that specific biochemical.
We have decided, however, to treat in the data model only derivatives in the narrower sense, i.e. not character data as derivatives, but in the interest of user convenience, a joint visualization of derivatives and character datasets in the user interface independent of the model decision is possible.
For convenience, the results can be copied to the visualization query window for quick and easy inspection.
The visualization does not require a separate installation effort (a manageability convenience for users) and the architecture provides a platform-independent access regardless of the operating system or browser that is run on the user machine.
For production use by a wide community of computational scientists, many convenience functions would have to be added: a code and data editor, data visualization, data management, etc.
NGS-cancer tools for the convenience have been categorized into cancer genomics, cancer transcriptomics, cancer epigenomics, quality control and visualization.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com