Question: How to extract normalized matrix after using calcNormFact function (with TMM method) ? edgeR
0
gravatar for Katerina
2.2 years ago by
Katerina0
Katerina0 wrote:

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() ?

rna-seq edger R • 798 views
ADD COMMENTlink modified 18 months ago by kristoffer.vittingseerup3.4k • written 2.2 years ago by Katerina0

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

Question: edgeR TMM values

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by h.mon31k
0
gravatar for kristoffer.vittingseerup
18 months ago by
European Union
kristoffer.vittingseerup3.4k wrote:
cm <- edgeR::cpm(data0)

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

ADD COMMENTlink written 18 months ago by kristoffer.vittingseerup3.4k
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