Entering edit mode
5.8 years ago
Katerina
•
0
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() ?
This has been asked before here end elsewhere, e.g., see this thread:
Question: edgeR TMM values