[BioC] default fdr rate in limma/affylmgui

[James W. MacDonald]

Hi Karl,

k. brand wrote:
> Dear List,
> 
> I'm trying to confirm the default fdr rate (for the BH method) in limma 
> & also in affylmGUI. I failed to extract this information from list 
> archives or the manual.

That is a pretty broad question. What particular function are you 
talking about? I don't know that you can assume all functions in both 
packages that adjust for multiplicity use the same correction.

However, this info can be had in (at least) two ways. Say you want to 
know about topTable().

?topTable gives me

Usage:

 
topTable(fit,coef=NULL,number=10,genelist=fit$genes,adjust.method="BH",sort.by="B",resort.by=NULL,p.value=1,lfc=0)

Further, args() gives me this:

 > args(topTable)
function (fit, coef = NULL, number = 10, genelist = fit$genes,
     adjust.method = "BH", sort.by = "B", resort.by = NULL, p.value = 1,
     lfc = 0)

You could also just type topTable at an R prompt and scroll back to the 
top of the function to see what the defaults are.

Best,

Jim


> 
> Does anyone know what it defaults to when not specified? And out of 
> curiosity, where/how is this information obtained/confirmed?
> 
> thanks in advance,
> 
> Karl
> 
> 

-- 
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