edgeR之TMM标准化

library(edgeR)
library(ggplot2)
data <- read.delim('../mouse_TPM_notCross.matrix.xls', row.names = 1, sep = '\t', check.names = FALSE)
group <- factor(rep(c('A', 'B', 'C'), each = 3))
y <- DGEList(counts = data, group = group)
y <- calcNormFactors(y)
logcpm <- cpm(y, prior.count=3, log=TRUE)
write.table(logcpm, file="mouse_TMM.xls", sep="\t", quote=F, row.names=T, col.names=T)
#dgList <- estimateCommonDisp(y)
#dgList <- estimateTagwiseDisp(dgList)
#norm_counts.table <- t(t(dgList$pseudo.counts)*(dgList$samples$norm.factors))
#write.table(norm_counts.table, file="mouse_gc_pareto_TMM.xls", sep="\t", quote=F)
#pheatmap(log(data+1),cluster_rows=T,cluster_cols=T,scale="none",border_color="white",color=colorRampPalette(rev(c("red","white","blue")))(102))

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