how dose the log2FoldChange is calculated by DESeq2

[aoe0618]

hello!
I did four samples RNA-seq experiment, it made me confused when get into differential expressed gene analysis by R package DESeq2.
I can't figure out how dose the log2FoldChange is calculated.
here one example:
geneID basemeanA basemeanB log2FoldChange
c46711_g1 1.99888849285605 17999.4664972886 10.406824704617

not equal to this formula log2(basemeanB/basemeanA) result;
anyhelp is appreciated!

Thanks!

[dpryan]

DESeq2 uses shrunken fold-changes, so you shouldn't expect the reported value to match what you manually calculate. I'll add that it becomes rather difficult to manually calculate things with more complicated designs.

[Michael Love]

hi aoe0618, check the documentation

?DESeq

or the vignette

browseVignettes("DESeq2")

or the manuscript (linked on first page of the vignette)