Perform normalization to GeoMX data

geomxNorm(
  spe_object,
  method = c("TMM", "RPKM", "TPM", "CPM", "upperquartile", "sizefactor"),
  log = TRUE
)

Arguments

spe_object: A SpatialExperiment object.
method: Normalization method to use. Options: TMM, RPKM, TPM, CPM, upperquartile, sizefactor. RPKM and TPM require gene length information, which should be added into rowData(spe). Note that TMM here is TMM + CPM.
log: Log-transformed or not.

Value

A SpatialExperiment object, with the second assay being the normalized count matrix.

References

Robinson, M. D., McCarthy, D. J., & Smyth, G. K. (2010). edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics, 26(1), 139-140.

Love, M., Anders, S., & Huber, W. (2014). Differential analysis of count data–the DESeq2 package. Genome Biol, 15(550), 10-1186.

Examples

data("dkd_spe_subset")

spe_tmm <- geomxNorm(dkd_spe_subset, method = "TMM")
spe_upq <- geomxNorm(dkd_spe_subset, method = "upperquartile")
spe_deseqnorm <- geomxNorm(dkd_spe_subset, method = "sizefactor")