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PCA task and data nodes will be generated.

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Because the upstream PCA task was performed separately for each sample, the t-SNE task will also be performed separately for each sample. t-SNE task and data nodes will be generated (Figure 5).

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Numbered figure captions
SubtitleText Name the cell-level attribute AnchorName Classifiy attribute name

A new task, Classify, is added to the Analyses tab. This task produces a new Classify result data node (Figure 20).The new attribute is stored in the Data tab and is available to any node in the project.

• Click on the Glioma (multi-sample) project name at the top to go back to the Analyses tab
• Your browser may warn you that any unsaved changes to the data viewer session will be lost. Ignore this message and proceed to the Analyses tab

• Double-click the new Classify result data node to open the task report (Figure 21)

The Classification summary table shows a breakdown of the number of glioma cells that were classified per sample. The cells that were not classified are labeled N/A.

The Top marker features per label table shows the top 10 upregulated genes in each cell type. In this case, the glioma cells are compared to the N/A cells using ANOVA and the genes are filtered for fold-change >1.5 and sorted by descending fold-change values. To obtain the full list of biomarker genes with p-values and fold-changes, click the Download link in the bottom right of the table.

One multi-sample t-SNE plot

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The PCA task will run as a new green layer.

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Once the task has completed, we can view the plot.

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A new task, Classify, is added to the Analyses tab. This task produces a new Classify result data node in a green layer (Figure 32).The new attribute is now available for downstream analysis.

• Click on the Glioma (multi-sample) project name at the top to go back to the Analyses tab
• Your browser may warn you that any unsaved changes to the data viewer session will be lost. Ignore this message and proceed to the Analyses tab

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