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The trajectory should be built using a set of genes that increase or decrease as a function of progression through the biological processes being modeled. One example is using differentially expressed genes between cells collected at the beginning of the process to cells collected at the end of the process. If you have no prior knowledge about the process being studied, you can try identifying genes that are differentially expressed between clusters of cells or genes that are highly variable within the data set. Generally, you should try to filter to 1,000 to 3,000 informative genes prior to running Trajectory analysis. The list manager functionality in Partek Flow is useful for creating a list of genes to use in the filter. To learn more about list management, please see List management. 

Parameters

Dimensionality of the reduced space

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