Output Description

Batch Normalization

Running this process using the LungCancerExample sample setting generates the tabbed Results window shown below. Refer to the Batch Normalization process description for more information. Output from the process is organized into tabs. Each tab contains one or more plots, data panels, data filters, and so on. that facilitate your analysis.

The Results window contains the following panes:

Tab Viewer

This pane provides you with a space to view individual tabs within the Results window. Use the tabs to access and view the output plots and associated data sets.

The following tabs are generated by this process:

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PCA Plot: This tab shows an interactive three-dimensional scatterplot of principal components for each batch before and after normalization.

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Variance Components Chart (Batch Normalization): This tab shows bar charts illustrating principal variance components for each batch.

Output Data

This process generates the following data sets:

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Batch Normalized Output Data Set: This output data set contains the batch normalized data. This data set is indicated by the _bnm suffix. Click Open to view the data set.

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Batch Profile Output Data Set: This data set (indicated by the _bns suffix) provides the parameters used for normalizing the data in the input data set. These parameters can also be used for normalizing data from subsequent studies and for estimating an updated batch profile. Click Open to view the data set.

For detailed information about the files and data sets used or created by JMP Genomics software, see Files and Data Sets.

General

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Click View Data to surface the data sets corresponding to the active tab.

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Click Reopen Dialog to reopen the completed process dialog used to generate this output.

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Click Create Report to generate a pdf- or rtf-formatted report containing the plots and charts of selected tabs.

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Click Close All to close all graphics windows and underlying data sets associated with the output.