James W. MacDonald
jmacdon at med.umich.edu
Thu Feb 21 16:44:23 CET 2008
Not having used the twilight package before, I took a quick look at the
help page for both twilight() and twilight.pval() and it seems obvious
that the functions do two completely different things. Have you looked
at the help pages? That would seem to be a reasonable place to start.
See ?twilight and ?twilight.pval
In addition, this package comes with a vignette that discusses both
functions and what you use them for. Again, this would be a reasonable
thing to peruse. After loading the package try openVignette() and choose
the twilight vignette.
Mahdi Osman wrote:
> Dear list,
> I am trying to understand how the package "twilight" works.
> Version: 1.14.1 Title: Estimation of local false
> discovery rate
> I worked out the example given in the package according to the
> guidelines given. I also tried another run using my own real dataset.
> I am very much interested in getting to understanding a bit more
> about individual outputs of the twilight package. When I execute the
> function "twilight.pval" I get among other things the "result"
> dataframe. I also get the "result" dataframe when I execute the
> function "twilight". I spent a bit of time to figure out if there is
> a difference between the two, ie, "result" from "twilight.pval" and
> "twilight" functions, respectively. I also flipped through the
> guidelines, but could not find a hint on why the "result" dataframe
> is returned in both cases and whether or not there is a difference
> between the two datarames. I would appreciate if anyone can give me
> further hint on when to use "twilight.pval" and "twilight" functions.
> Thanks for your hint in advance.
> Mahdi Osman
James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
Ann Arbor MI 48109
More information about the Bioconductor