I was trying to use NanoTube and NanoStringDiff packages to normalize my NanoString RNA seq data. We incorporate the panel standards to address the batch effect but I don’t know how to use these two packages to normalize the data incorporating the panel standards. Alternatively, if I use nSolver (NanoString designed GUI software) to normalize the data, can I use packages such as limma or DESeq2 to perform differential expression on the normalized count matrix?

Here’s the info of panel standard and the two packages. I’ve read through the vignettes and manuals but couldn’t find info to incorporate panel standards in these two packages.

Panel Standard

NanoTube

NanoStringDiff