Clinical data have individual differences and it often makes detecting changes difficult. If you can make pairs of samples from same patients, you can cancel individual difference and focus on effects of the parameter. Paired T-test cancels the variance in control samples, and takes only effect of the parameter. As a result, power of test improves by in general.
To apply paired T-test on Subio Platform, you need to define pairs and divide by control samples in each pair by setting of "Ratio to Control Samples" normalize block. And then apply "Compare to Control" tool of Basic Plug-in.
How to Perform a Paired t-test in Subio Platform｜Setting Patient-Matched Control Samples
In this video, Centering is turned off, and Ratio to Control Samples is used to create ratios using the control sample within each patient as the reference. When there are many samples, Define Groups by Parameter can be used to efficiently set patient-matched control samples.
Finally, the generated ratio data is used in the Compare to Control tool to perform a comparison corresponding to a paired t-test and export a DEG list.