[https://www.nanostring.com/products/analysis-solutions/ncounter-analysis-solutions/ Download nSolver], follow [https://www.nanostring.com/products/analysis-solutions/ncounter-analysis-solutions/nsolver-data-analysis-support/?gclid=CjwKCAiA6Y2QBhAtEiwAGHybPXRmTMsg6CYmYlPJl4DtBPbgD83x2YhVeUUxBMgr2fadqt_7P-WSKRoCyZgQAvD_BwE nSOlver guide ] for Check QC, normalization and analysis. 

  For mRNA normalization, nSolver first checks on positive controls, and then normalizes housekeeping genes with geometric mean.
 
  The reported ratio is fold change, with the higher value as numerator, sign as direction of the comparison.