the results of logFC is base e (log(FC,base=exp(1)) or base 2 (log2FC) ,is logFC same as log2FC in edgeR?
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ZihaoXing • 0
@zihaoxing-13254
Last seen 3.9 years ago

i found that the fold change of different RNAseq expression analyse resultsĀ  in edgeR is logFC, log2FC is also often used in other analysed ,i want to know if the logFC is same as log2FC in edgeR ,or it is based on exp(1).

edger limma logfc • 1.7k views
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@gordon-smyth
Last seen 1 hour ago
WEHI, Melbourne, Australia

Results reported by edgeR are always log2 so, yes, logFC is the same as log2FC in edgeR.

The use of base2 for log-fold-changes is usual practice in the bioinformatics literature and in most Bioconductor packages.

edgeR uses loge internally, but results are always converted to log2 for reporting.

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thanks ,i hope it can be changed into log2FC in edgeR in future ,otherwise, it is easy to be confused ,because log default as loge rather than log2 in math.

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