Partek Flow Documentation

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  • Select the Gene counts data node
  • Select Normalization and scaling from the task menu
  • Select Normalize counts from the Normalization and scaling section of the task menu (Figure 1)

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SubtitleTextInvoking Normalize counts
AnchorNameInvoking Normalize Counts

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The Read count normalization menu will open (Figure 2).

 

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SubtitleTextRead counts normalization task menu
AnchorNameRead counts normalization

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Normalization can be performed by sample or by feature. By sample is selected by default; this is appropriate for the tutorial data set. 

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This adds Total count and Add 0.0001 to the Normalization order panel (Figure 3). Normalization steps are performed in descending order

 

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SubtitleTextRecommended normalization settings
AnchorNameRecommended normalization settings

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Total Count normalizes read counts for each gene by the total count of the sample. This accounts for differences in total read counts between samples. 

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A Normalize counts task node and a Normalized counts data node are added to the pipeline (Figure 4)

 

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SubtitleTextNormalize counts task node and Normalized counts data node
AnchorNameNormalize counts and Normalized counts nodes

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