normalize_housekeeping {NanoTube} | R Documentation |
Scale endogenous genes by the geometric mean of housekeeping genes. This should be conducted after positive control normalization and background correction. This step is conducted within processNanostringData, when normalization is set to "nCounter".
normalize_housekeeping(dat, genes = NULL, logfile = "")
dat |
NanoString data, including expression matrix and gene dictionary. |
genes |
List of housekeeping genes to use for normalization. If NULL (default), will use all genes marked as "Housekeeping" in codeset. |
logfile |
Optional name of logfile to print messages, warnings or errors. |
NanoString data, with expression matrix now normalized by housekeeping gene expression.
example_data <- system.file("extdata", "GSE117751_RAW", package = "NanoTube") # Load data, positive control normalization, and background filtering dat <- read_merge_rcc(list.files(example_data, full.names = TRUE)) dat <- normalize_pos_controls(dat) dat <- remove_background(dat, mode = "t.test", pval = 0.05) # Normalize by genes marked "Housekeeping" in RCC files dat <- normalize_housekeeping(dat) # Normalize by specified housekeeping genes (gene symbol or accession) dat <- normalize_housekeeping(dat, genes = c("TUBB", "TBP", "POLR2A", "GUSB", "SDHA"))