[BioC] RE : Re: sam and the new version

[Holger Schwender]

If ebam.out is the output of ebam und you want to use delta=0.9 as the minimum posterior probability for your genes to be called differentially expressed, then

> summary(ebam.out, delta = 0.9)

returns the genes called differentially expressed with other useful statistics as their z-value and their local FDR, but no raw p-value is returned as in sam.

If you are just interested in the names of this genes you can also use

> list.siggenes(ebam.out, 0.9)

Best,
Holger

-------- Original-Nachricht --------
Datum: Fri, 20 Jul 2007 09:04:38 +0200 (CEST)
Von: el mousselly antra <elmousselly.antra at yahoo.fr>
An: Holger Schwender <holger.schw at gmx.de>
CC: bio c bioconductor <bioconductor at stat.math.ethz.ch>
Betreff: RE : Re: sam and the new version

>  
>   hi holger,
>   1.yes siggenes work well, the problem was in the 
> version i use an old version.there is no problems now
>   2.but i have an other problem to have a list of genes DE on 
> ebam and also p-value for each genes i don't know how 
> because in the vignette i don't see something that explain this 
> you talk just about number of genes DE but 
> list of genes DE ???
>   thanks 
> best wishes
>   elmousselly antra 
> 
> Holger Schwender <holger.schw at gmx.de> a écrit :
>   Actually, I do not know anymore what works in 1.2.0 and not in 1.2.11,
> as these are pretty old versions which have been updated several times with
> many major changes. Please use the current version of siggenes, version
> 1.10.1.
> 
> And please let me then know if something does not work in this version.
> And if yes, what does not work.
> 
> If you do not know how to specify the arguments/options in the function,
> please take a look in the vignette of siggenes:
> 
> > vignette("siggenes")
> 
> Almost everything is explained in this vignette (and what is not explained
> in the vignette is explained in the R News article mentioned -- with link
> -- in the vignette).
> 
> Thanks,
> Holger
> 
> -------- Original-Nachricht --------
> Datum: Thu, 19 Jul 2007 09:17:34 +0200 (CEST)
> Von: el mousselly antra 
> An: holger.schw at gmx.de
> CC: bio c bioconductor 
> Betreff: sam and the new version
> 
> > dear schwender,
> > i am using sam in siggens but i have some problems
> > some functions don't work as i have the habit to use it, like
> > summary(sam.out)
> > sum.sam.out <- summary(sam.out, 0.4, ll = FALSE)
> > sum.sam.out at mat.sig
> > only function sam work well but a lot of functions functions 
> > have some problems or changes that i don'know how but i think
> > in the version 1.2.0 in the past 
> > have worked but now this new version d'ont work in the version 1.2.11
> > i don't know what'the problem and what's i have to do
> > thank you 
> > sincerly
> > 
> > 
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