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By clicking on Optional columns, you can retrieve more annotation if there are any more annotation information in the annotation model you specified for quantification, like genomic location, strand information etc.

On the right of each contrast header, there is volcano plot icon ( ). Select it to display the volcano plot on the chosen contrast (Figure 11).

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If lognormal with shrinkage method was selected for GSA, a shrinkage plot is generated in the report (Figure 13). The plot helps to determine the threshold of low expression features. X-axis shows the log2 value of average coverage. If there is an increase before a monotone decrease trend on the left side of the plot, you need to set a higher threshold on the low expression filter, detailed information on how to set the threshold can be found from GSA white paper.

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