[BioC] called genes after SAM anaylsis

[Holger Schwender]

Hi Gregor,

use, e.g., the function list.siggenes, i.e.

> list.siggenes(sam9,0.9)

to obtain the gene names. You can also use something like 

> summary(sam9,0.9)

There you also get the gene names and additionally some statistics.

This is, however, also explained in the vignette of siggenes. You can open
this vignette by

> vignette("siggenes")

or if you use siggenes_1.4.0 (that's the BioC 1.7 version) under Windows,
click on

Vignettes --> siggenes --> siggenes

Best,
Holger



> --- Ursprüngliche Nachricht ---
> Von: "M a r c e l" <benco81 at hotmail.com>
> An: bioconductor at stat.math.ethz.ch
> Betreff: [BioC]  called genes after SAM anaylsis
> Datum: Wed, 02 Nov 2005 16:33:11 +0100
> 
> Hi there!
> 
> My aim was to get about 100 called genes out of the sam analysis which I 
> have achieved doing this:
> 
> >sam9 <- sam(filtered, cl, delta=0.9, rand=2)
> 
> the delta of 0.9. gives me 120 Called genes:
> 
> >sam9
> SAM Analysis for the Two-Class Unpaired Case Assuming Unequal Variances
> 
>   Delta      p0   False  Called     FDR
>   0.900   0.570   8.920 120.000   0.042
> 
> and I now want to get all the Called genes to perform further anaylsis 
> (heatmap and so on). how can I do that?
> 
> I´ve tried several things like:
> 
> called <- sam9$Called
> 
> but with no success.
> 
> Thanks to everyone!
> 
> cheers,
> gregor
> 
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