9 Normalising CosMx data”

Data normalisation is a tricky step. There are multiple opinions about it in the feild. Tools such as SpaNorm have been specifically developed for normalising image-based spatial transcriptomics data. However, for this data set, I foudn out that LogNormalise actually work well. So that is what Im doing below. But depending on the data structure, LogNormalise may not work for your data.

merged <- NormalizeData(
                    merged,
                    normalization.method = "LogNormalize",
                    verbose = TRUE, 
                    scale.factor = 10000,
                    assay = "RNA")

Challenge: Explore the functionality of SpaNorm together.