the distribution of M values
TMM normalization is a simple and effective method for estimating relative RNA production levels from RNA-seq data
The TMM method estimates scale factors between samples that can be incorporated into currently used statistical methods for DE analysis.
We have shown that normalization is required in situations where the underlying distribution of expressed transcripts between samples is markedly different
In essence, both microarray and TMM normalization assume that the majority of genes, common to both samples, are not differentially expressed
two RNA populations, A and B
Scaling to library size as a form of normalization makes intuitive sense
suppose every gene that is expressed in B is expressed in A with the same number of transcripts
The distribution of M values for these technical replicates is concentrated around zero.
The M versus A plot in Figure 1c illustrates that there exists a prominent set of genes with higher expression in liver
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