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SubtitleText | Navigating to the differential analysis options |
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AnchorName | Differential analysis |
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Select the appropriate differential analysis method (Figure 2). In this tutorial we are going to use GSA, but Partek® Flow® offers a number of alternatives. Hover the mouse over the
symbol for more information on each differential analysis method, or see our Differential Analysis user guide for a more in-depth look.
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SubtitleText | Select the method for differential analysis from the options provided. |
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AnchorName | Method choice |
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The Included attributes page shows all available attributes for analysis (Figure 3). Here, we only have one attribute, 5-AZA Dose.
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SubtitleText | The Comparison selector allows multiple comparisons to be designed and added |
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AnchorName | Comparison selector |
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It is easiest to think about comparisons as the questions we are asking. In this case, we want to know what are the differentially expressed genes between untreated and treated cells. We can ask this for each dose individually and for both collectively.
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SubtitleText | Designing a comparison to add |
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AnchorName | Adding comparisons |
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- Repeat to create comparisons for 10μM vs. 0μM and 5μM:10μM vs. 0μM (Figure 6)
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SubtitleText | Comparisons for 5uM vs. 0uM, 10uM vs. 0uM, and 5uM:10uM vs. 0uM have been added |
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AnchorName | Comparisons set up |
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By default, the GSA will use a lognormal with shrinkage model for its analysis of variance of each gene. This is appropriate for most data sets and will tend to give accurate and reproducible results. To learn more about the advanced options available in the GSA task, please see the GSA user guide.
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SubtitleText | Gene analysis task node and Feature list data nodes |
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AnchorName | Gene analysis task node |
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