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Question: 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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gravatar for ZihaoXing
11 weeks ago by
ZihaoXing • 0
ZihaoXing • 0 wrote:

i found that the fold change of different RNAseq expression analyse results  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).
limma logfc edger
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modified 11 weeks ago by Gordon Smyth ♦ 35k • written 11 weeks ago by ZihaoXing • 0
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gravatar for Gordon Smyth
11 weeks ago by
Gordon Smyth ♦ 35k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth ♦ 35k wrote:

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.
ADD COMMENT • link modified 11 weeks ago • written 11 weeks ago by Gordon Smyth ♦ 35k

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.

ADD REPLY • link written 11 weeks ago by ZihaoXing • 0
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