[BioC] Can logFC be used to determine effect size?

[Gordon K Smyth]

Dear Jack,

> Date: Fri,  9 Aug 2013 02:02:31 -0700 (PDT)
> From: "Jack [guest]" <guest at bioconductor.org>
> To: bioconductor at r-project.org, jukka.alasaari at thl.fi
> Subject: [BioC] Can logFC be used to determine effect size?
>
> Hello,

> I am trying to work out the meaning of logFC in the toptable from limma 
> package.  Some sources say that it is the log2 of FC

The best way to find out what something means is to read the 
documentation.

If you want to know what logFC is from toptable, then open the help page 
help("toptable") and scan down for the entry for logFC, which says:

"logFC: estimate of the log2-fold-change corresponding to the effect or 
contrast"

Every output quantity is carefully documented in this way.

> and others say that it is not.

What sources say this?

Gordon

> Is this value the actual difference in averages of cases and controls 
> (and as such can it be used to determine effect size)?
>
> Regards,
> Jack

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