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
14 months 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 edger logfc • 345 views
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modified 14 months ago by Gordon Smyth ♦ 39k • written 14 months ago by ZihaoXing • 0
Answer: the results of logFC is base e (log(FC,base=exp(1)) or base 2 (log2FC) ,is logFC
1
gravatar for Gordon Smyth
14 months ago by
Gordon Smyth ♦ 39k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth ♦ 39k 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 14 months ago • written 14 months ago by Gordon Smyth ♦ 39k

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 14 months ago by ZihaoXing • 0
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