Hello everyone, I'm a beginner in data processing and struggling with one particular case. I downloaded the GSE139255 dataset from GEO NCBI, and during analysis in R I realized extensive distribution of values before and after the log2 transformation1. Can you help me how to normalize the data? Also, in some other cases, I realized that set of samples has a uniform but higher distribution than another set of samples 2. Both samples can be seen in the attached plots.

You could try getting the RCC files and normalizing yourself, using getGEOSuppFiles and the NanoStringNorm package. Or just use NanoStringNorm to read the data in, and normalize using regular methods from edgeR or DESeq2.