How to normalize RNA-seq when 50% genes are DE? (TMM)
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natalia_lt • 0
@natalia_lt-20482
Last seen 2.5 years ago
Barcelona

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?

limma TMM differential expression normalization rnaseq • 306 views
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@james-w-macdonald-5106
Last seen 16 hours ago
United States

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

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