Question

the results of logFC is base e (log(FC,base=exp(1)) or base 2 (log2FC) ,is logFC same as log2FC in edgeR?

0

Entering edit mode

ZihaoXing • 0

@zihaoxing-13254

Last seen 5.4 years ago

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).

edger limma logfc • 3.2k views

ADD COMMENT • link updated 15 months ago by Gordon Smyth 50k • written 5.6 years ago by ZihaoXing • 0

score 1 · Answer 1 · 2018-09-25

1

Entering edit mode

Gordon Smyth 50k

@gordon-smyth

Last seen 5 hours 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.

ADD COMMENT • link 5.6 years ago Gordon Smyth 50k

0

Entering edit mode

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 5.6 years ago ZihaoXing • 0

0

Entering edit mode

I prefer the more concise logFC notation and I don't think there's any ambiguity in the edgeR context. Any of the edgeR help pages will tell you that the fold-changes are log2.

log typically means log2 in both computer science and bioinformatics, and the standard international notation for loge is ln() rather htan log() (https://en.wikipedia.org/wiki/Logarithm) so I don't think you can be pedantic that log means loge.

ADD REPLY • link 15 months ago Gordon Smyth 50k