[BioC] sum.sam.out

[Nicolas Servant]

hi,

try to first extract your matrix or other elements, with :
 mat <- attr(data.out.sum,"mat.sig")
and then, access it with :
mat$Row

Nicolas S.


Assa Yeroslaviz wrote:

>hi,
>
>can someone please explain to me, why is it, that I'm always getting the NULL-
>value when I try to look fot the significance genes:
>  
>
>>data.out
>>    
>>
>SAM Analysis for the Two-Class Unpaired Case Assuming Unequal Variances
>
>   Delta    p0   False Called   FDR
>1    0.1 0.321 8323.01  14987 0.178
>2    2.2 0.321  395.88   5892 0.022
>3    4.4 0.321    2.78    628 0.001
>4    6.5 0.321    0.09     86 0.000
>5    8.6 0.321    0.01     14 0.000
>6   10.7 0.321    0.00      5 0.000
>7   12.9 0.321    0.00      2 0.000
>8   15.0 0.321    0.00      2 0.000
>9   17.1 0.321    0.00      1 0.000
>10  19.2 0.321    0.00      1 0.000
>
>  
>
>>data.out.sum <- summary(data.out,10)
>>data.out.sum
>>    
>>
>SAM Analysis for the Two-Class Unpaired Case Assuming Unequal Variances
>
>s0 = 0
>
> Number of permutations: 100
>
> MEAN number of falsely called genes is computed.
>
> Delta: 10
> cutlow: -23.092
> cutup: 15.556
> p0: 0.321
> Significant Genes: 6
> Falsely Called Genes: 0
> FDR: 0
>
>
>Genes called significant (using Delta = 10):
>
>    Row d.value  stdev p.value q.value       R.fold      Name
>1  4431  26.001  5.918       0       0 1.276614e+42 254466_at
>2 22511 -23.092 16.129       0       0 0.000000e+00 259927_at
>3  8199  18.353  5.608       0       0 1.826403e+25 249456_at
>4 14510  16.811  8.989       0       0 8.938649e+40 258067_at
>5  8351  16.391 10.682       0       0 3.078096e+46 252077_at
>6 16295  15.556  4.648       0       0 2.218854e+20 263441_at
>
>now, when I'm try to extract the information, I get:
>  
>
>>AE0625419.sum.out$row.sig.genes
>>    
>>
>NULL
>  
>
>>AE0625419.sum.out$mat.fdr
>>    
>>
>NULL
>  
>
>>AE0625419.sum.out$mat.sig
>>    
>>
>NULL
>
>Can anyone please tell me, how can i reach these values?
>
>THX
>
>Assa
>--
>Assa Yeroslaviz
>Lötzenerstr. 15
>51373 Leverkusen
>
>_______________________________________________
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>Bioconductor at stat.math.ethz.ch
>https://stat.ethz.ch/mailman/listinfo/bioconductor
>
>
>
>  
>


-- 
Nicolas Servant
Equipe Bioinformatique
Institut Curie 
26, rue d'Ulm - 75248 Paris Cedex 05 - FRANCE

Email: Nicolas.Servant at curie.fr
Tel: 01 44 32 42 75