[BioC] Problem in limma-voom

[Steve Lianoglou]

Hi,

On Wed, Feb 19, 2014 at 7:13 AM, Ming Yi <yi02 at hotmail.com> wrote:
> By the way, a small quick question: in the topTable result of limma, the logFC is base 2 or is natural base (2.71828 etc)? I though was base 2, just want to confirm.

Take a look at the help file from ?topTable under the Value section,
which is where the output is described.

Specifically, for the logFC output:

"""
estimate of the log2-fold-change corresponding to the effect or
contrast (for topTableF there may be several columns of
log-fold-changes)
"""

-steve

-- 
Steve Lianoglou
Computational Biologist
Genentech