Could anyone help me understand how edgeR calculates fold change?
Experimental set up:
RNA-Seq using illumina with 2 identical bacterial strains - one wild-type and one with a single gene deletion. We did not sequence biological replicates for this experiment so I only have one set of count data for each strain.
I set the dispersion to 0.1 as outlined in the EdgeR materials for identical strains.
I get the following output for a gene and I don't understand why
GeneID WTcount mutantcount logFC logCPM p-value
7872684 2291 7671 -0.271135002 13.11904664 0.679110027
This should be ~3-fold increase, definitely not a decrease. Maybe I'm missing something.
Experimental set up:
RNA-Seq using illumina with 2 identical bacterial strains - one wild-type and one with a single gene deletion. We did not sequence biological replicates for this experiment so I only have one set of count data for each strain.
I set the dispersion to 0.1 as outlined in the EdgeR materials for identical strains.
I get the following output for a gene and I don't understand why
GeneID WTcount mutantcount logFC logCPM p-value
7872684 2291 7671 -0.271135002 13.11904664 0.679110027
This should be ~3-fold increase, definitely not a decrease. Maybe I'm missing something.
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