Question: How to normalize RNA-seq when 50% genes are DE? (TMM)
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gravatar for natalia_lt
6 months ago by
natalia_lt0
Barcelona
natalia_lt0 wrote:

Hi, I'm analyzing RNAseq in order to identify differential expressed genes between 2 conditions in 15 individuals (total of samples = 30). The normalization method that I use is TMM, with Limma R package, using voom and duplicateCorrelations for the individuals. The problem is that in the analysis I obtain 50% of the genes differentially expressed (around 10.000 DE of 20.000 genes). The assumptions of the TMM normalization are violated. How to proceed with such a case?

ADD COMMENTlink modified 6 months ago by James W. MacDonald51k • written 6 months ago by natalia_lt0
Answer: How to normalize RNA-seq when 50% genes are DE? (TMM)
1
gravatar for James W. MacDonald
6 months ago by
United States
James W. MacDonald51k wrote:

This has been answered here more than once. An example being this.

ADD COMMENTlink written 6 months ago by James W. MacDonald51k
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