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?
Question: How to normalize RNA-seq when 50% genes are DE? (TMM)
6 weeks ago by
natalia_lt • 0
natalia_lt • 0 wrote:
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