[BioC] called genes after SAM anaylsis
Holger Schwender
holger.schw at gmx.de
Wed Nov 2 17:55:28 CET 2005
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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