Partek Flow Documentation

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  • Click the Single cell data node produced by the Filter cells task
  • Click Filtering in the task menu
  • Click Filter features (Figure 20)

 

 


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SubtitleTextInvoking Filter features
AnchorNameInvoking Filter features

There are three categories of filter available - Noise reduction filters, Statitics bsaed filters, and Feature list filters (Figure 21).

 

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SubtitleTextViewing the filtering options
AnchorNameFilter types

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The Noise reduction filter allows you to exclude genes considered background noise based on a variety of criteria. The Statistics based filters are useful for focusing on a certain number or percentile of genes based on a variety of metrics, such as variance. The Feature list filter allows you to filter your data set to include or exclude particular genes.

We will use a Noise reduction filter to exclude genes that are not expresed by any cell in the data set, but were included in the matrix file.

  • Click the Noise reduction filter check box 
  • Set the Noise reduction filter to Exclude features where expression value == 0 in 100% of cells using the drop-down menus and text boxes (Figure 22)
  • Click Finish to apply the filter

 

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SubtitleTextConfiguring a noise reduction filter to exclude genes not expressed in the data set
AnchorNameConfiguring a noise reduction filter

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This produces a Filtered counts data node. This will be the starting point for the next stage of analysis - identifying cell types in the data using the interactive t-SNE plot. 

 

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