Flow Documentation

Partek Flow Documentation

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Table of Contents
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t-SNE (t-distributed stochastic neighbor embedding) is a visualization method commonly used analyze single-cell RNA-Seq data. Each cell is shown as a point on the plot and each cell is positioned so that it is close to cells with similar overall gene expression. When working with multiple samples, a t-SNE plot can be drawn for each sample or all samples can be combined into a single plot. Viewing samples individually is the default in Partek Flow Partek® Flow® because sample to sample variation and outlier samples can obscure cell type differences if all samples are plotted together. However, as you will see in this tutorial, in some data sets, cell type differences can be visualized even when samples are combined.

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The number of selected cells is indicated in the Selection section of the menu.

  • Select Classify selection (Figure 12)

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Numbered figure captions
SubtitleTextThe number of cells in each classification is displayed in the classification section.
AnchorNameViewing classifications

Classifications made on the t-SNE plot are retained as a draft after you exit the t-SNE task report. The Save Apply classifications button runs a task, Classify cells, which generates a new Classified cells data node. In this tutorial, we will classify malignant cells for each sample before we save the classifications, but if necessary, you can exit the t-SNE task report and continue classifying the next sample later. 

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