nSolver normalization method multiplies endogenous gene counts with the mean of Geomean of housekeeping gene counts.
Would not mean(pcG) and mean(hkG) cause cartridge-specific batch effect as the mean value will be depending on how many samples you are using in the normalization process?
And they also make nSolver option unsuitable for the normalization of only one sample as mean(hkG)/hkG will be 1, and it will ignore the housekeeping genes.
nSolver normalization method multiplies endogenous gene counts with the mean of Geomean of housekeeping gene counts.
Would not mean(pcG) and mean(hkG) cause cartridge-specific batch effect as the mean value will be depending on how many samples you are using in the normalization process?
And they also make nSolver option unsuitable for the normalization of only one sample as mean(hkG)/hkG will be 1, and it will ignore the housekeeping genes.
https://github.com/Nanostring-Biostats/NanoStringNCTools/blob/master/R/NanoStringRccSet-normalize.R
Best wishes Cankut