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 -- :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: Mahdi Osman (PhD) E-mail: m_osm at gmx.net :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: "Making the simple complicated is commonplace; making the complicated simple, awesomely simple, that's creativity." ~ Charles Mingus ~ ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::

Hi Mahdi, 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. Best, Jim 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. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623