Hi,
We have tried using Q3 and TMM normalisation for DSP WTA data. But when it comes to TCR spike-in add-on data, which normalisation methods (Q3, TMM or Poisson threshold model based normalisation in the GeoDiff) is applicable?
As the TCR data only contains probes for 146 variable and joining segments (number of genes a lot less than WTA), and expression levels vary among different TCR genes (assumption of TMM - most of the genes are not differentially expressed - may not hold in this setting).
Cheers!
Hi,
We have tried using Q3 and TMM normalisation for DSP WTA data. But when it comes to TCR spike-in add-on data, which normalisation methods (Q3, TMM or Poisson threshold model based normalisation in the GeoDiff) is applicable?
As the TCR data only contains probes for 146 variable and joining segments (number of genes a lot less than WTA), and expression levels vary among different TCR genes (assumption of TMM - most of the genes are not differentially expressed - may not hold in this setting).
Cheers!