Hi there, I know it is a old question about the normalization of count using edgeR TMM methods.And I know using calcNormFactor(DEGList, method = "TMM") to get norm.factors.But how can I get the normalized count matrix using some command.And I know the simple method is using every count to divide the its own norm.factors.But I think there are some command I don't know .Because I know the DESeq2 has the similar command . like estimateSizeFactors(dds) to get the sizeFactors .and Using sizeFactors(dds) can show the norm.factors like showing in DEGlist$samples$norm.factors.And DESeq2 has a command : counts(dds, normalized =T) to directly output the normalized count matrix.And I checked the normalized counts of every gene is using raw count to divide the corresponding sizeFactors. So I wonder if there is similiar command in edgeR to directly output the normalized count matrix? And I have tried the cpm() function. It didn't work like the principal of scaling factor do. Any ideals? Thanks in advance!
Question: how to get normalized count data from edgeR using TMM methods
11 days ago by
15958021290 • 0
15958021290 • 0 wrote:
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