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Yes, you can use the Compute biomarkers task to compare one subgroup at a time to all of the others combined. An alternative option is to set up the differential analysis model in this way; for more information please see the information here for each model. 

When I download the gene count from the output data node generated from quantify to annotation model task, why I can't find some of my genes of interest?

In quantify to annotation model dialog, by default, Partek Flow perform filter features based total count across all the samples, only features total count is greater than 10 will be reported. If you want to report all the genes in the annotation file, change the Filter features value to 0.

Biological Interpretation FAQs

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