Is normalized counts stored in "$pseudo.alt" after estimating common dispersion?
## edgeR run script library(edgeR) setwd("C:/Documents and Settings/user/My Documents/") # define input Expression file name to read input <- "test.exp.txt" # input Expression file raw.data <- read.delim(input) # read the sample columns d <- raw.data[,2:204] # Edit it accordingly # read row or gene names rownames(d) <- raw.data[,1] # define the groups group <- c(rep("A",68),rep("B",65),rep("C",70)) # Edit it accordingly ##edgeR stores data in a simple list-based data object called a DGEList. The function readDGE makes a DGEList object directly. d <- DGEList(counts = d, group=group) ## By default, calcNormFactors uses the TMM method and the sample whose 75%-ile (of library-scale-scaled counts) is closest to the mean of 75%-iles as the reference. d = calcNormFactors(d) ##To estimate common dispersion: ## The common dispersion is the "squared coefficient of variation", where the coefficient of variation gives the amount of variability in the true abundance for each gene between replicates #The square root of the common dispersion gives the coefficientcient of variation of biological variation (BCV)# d = estimateCommonDisp(d, verbose=TRUE) # Normalized counts ??? d$pseudo.alt # export Normalized counts table to a file write.table(d$pseudo.alt, file="TMM_edgeR_Normalized.test.exp.txt", row.names = TRUE, col.names = TRUE, sep = "\t" )