How to extract normalized matrix after using calcNormFact function (with TMM method) ? edgeR

Question

[Katerina]

Hi there,

I'm new and I apologize in advance for my naïve question.

I wanna get the normalized matrix after using the function calcNormFact with method TMM. Below there is my code.

matrice<-matrice_reads_five
classes_one<-as.factor(c(rep("1",3),rep("2",3)))
data0<-DGEList(counts=matrice,group=classes_one)
data0<-calcNormFactors(data0)
design_matrix<- model.matrix(~classes_one) 

data2.glm<-estimateGLMTrendedDisp(data0,design_matrix)
data2.glm<-estimateGLMTagwiseDisp(data2.glm,design_matrix)
fit2<-glmFit(data2.glm,design_matrix)
lrt2<-glmLRT(fit2,coef=2)
head(lrt2$table)

In the past posts someone said that it can be used the function cpm (). Is it correct? How can I extract the normalized data matrix used by the function estimateGLMTrendedDisp() ?

[h.mon]

This has been asked before here end elsewhere, e.g., see this thread:

Question: edgeR TMM values

Answer 1

[Kristoffer Vitting-Seerup]

cm <- edgeR::cpm(data0)

If you need log-transformed values you can make the cpm function calculate those as well