Seurat: avg_logFC - natural log or log 2?
I could not find this information in the documentation, but maybe I missed it: for the FindMarkers and FindAllMarkers functions is the avg_logFC in base 2 or natural log?
malosreet
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>All comments
Hi,
avg_logFC is returned in natural log. I guess that all log transformations in Seurat are performed using the natural log. Details on this can be found in the source code at lines 171 to 173, and at line 284 in differential_expression.R.
Best,
Leon
leonfodoulian
on 25 Feb 2018
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Most helpful comment
Hi,
avg_logFCis returned in natural log. I guess that all log transformations in Seurat are performed using the natural log. Details on this can be found in the source code at lines 171 to 173, and at line 284 in differential_expression.R.Best,
Leon