...

FDR is the expected proportion of false discoveries among all discoveries. FDR Step-up is a particular method to keep FDR under a given level, alpha, that was proposed in this paper. In Partek Flow, if one calls all of the features with p-values 0.02 or less, the FDR is less or equal to 0.41.

How to perform a paired t-Test in Flow

You should have at least the following two attributes in the Metadata, treatment (including two subgroups) and subject ID (to pair the two samples). When performing differential analysis, choose ANOVA and include both attributes into the ANOVA model, the two-way ANOVA is mathematically equivalent to paired t-Test.

...