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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
ZihaoXing0
ZihaoXing0 wrote:

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).

ADD COMMENTlink modified 11 weeks ago by Gordon Smyth35k • written 11 weeks ago by ZihaoXing0
1
gravatar for Gordon Smyth
11 weeks ago by
Gordon Smyth35k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth35k 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 COMMENTlink modified 11 weeks ago • written 11 weeks ago by Gordon Smyth35k

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 REPLYlink written 11 weeks ago by ZihaoXing0
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