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Nanostring-Biostats / GeoDiff

GeoDiff, an R package for count generating models for analyzing Geomx RNA data. Note that this version of the package is still under development, undergoing submission process to Bioconductor 3.14 release and still needs to complete NanoString internal verification process.
MIT License
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Normalisation methods for TCR spike-in add-on #38

Open qoiopipq opened 1 year ago

qoiopipq commented 1 year ago

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!

NicoleEO commented 1 year ago

Hi @qoiopipq,

Thank you for reaching out. Our customer support team will be able to help you with this. Please email support@nanostring.com with your question.

Thanks, Nicole