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exclude | Additional Assistance |
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Once we have performed GSA DESeq2 to identify differentially expressed genes, we can create a list of significantly differentially expressed genes using cutoff thresholds.
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The task report spreadsheet will open showing genes on rows and the results of the GSA DESeq2 on columns (Figure 1).
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SubtitleText | Viewing the GSA DESeq2 task report spreadsheet |
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AnchorName | Task report spreadsheet |
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To get a sense of what filtering thresholds to set, we can view a volcano plot for a comparison.
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SubtitleText | Viewing GSA DESeq2 results with a volcano plot |
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AnchorName | Volcano plot |
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Thresholds for the cutoff lines are set using the Significance card Statistics card (Configuration panel > Content Configure > SignificanceStatistics). The default thresholds are |2| for the X axis and 0.05 for the Y axis.
- Switch to the browser tab showing the GSA DESeq2 report
- Click FDR step up
- Click the triangle next to FDR step up to open the FDR step up options
- Leave All contrasts selected
- Set the cutoff value to 0.05. Hit Enter.
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Note that the number of genes that pass the filter is listed at the top of the filter menu next to Results: and will update to reflect any changes to the filter. Here, 32 27 genes pass the filter (Figure 3). Depending on your settings, the number may be slightly different.
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SubtitleText | Applying filters to the GSA DESeq2 results spreadsheet |
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AnchorName | Filtering a gene list |
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- Click Image RemovedImage Added to create a data node with only the genes that pass the filter
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SubtitleText | Filter list and a new Feature list node are added to the pipeline |
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AnchorName | Feature list data and task nodes |
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