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• Select Next to continue with 5-AZA Dose as the selected attribute

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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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• Repeat to create comparisons for 10μM vs. 0μM and 5μM:10μM vs. 0μM (Figure 6)
  
  

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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