Entering edit mode
SAURIN
★
1.1k
@saurin-799
Last seen 10.2 years ago
Dear BioC,
I am using siggenes package. If anyone have used,
please let me know, how can I get access of all
samoutput$fdr and samoutput$delta values from
samoutput object?
This might be very easy..but and even I have also
opened Vignette but there is not information in
Vignette as well.(sam.out$mat.fdr gives NULL)
I did following:
> samoutput <- sam(MatrixRMA,cl, rand = 123);
We're doing 90 complete permutations
>samoutput$mat.fdr
NULL
> samoutput
SAM Analysis for the Multi-Class Case with 3 Classes
Delta p0 False Called FDR
1 0.1 0.854 408.578 426 0.819
2 259.8 0.854 4.400 14 0.268
3 519.5 0.854 1.733 6 0.247
4 779.2 0.854 0.722 3 0.205
5 1038.9 0.854 0.333 2 0.142
6 1298.6 0.854 0.333 2 0.142
7 1558.3 0.854 0.333 2 0.142
8 1818.0 0.854 0.111 1 0.095
9 2077.7 0.854 0.111 1 0.095
10 2337.5 0.854 0.000 0 0.000
>summary(samoutput)
SAM Analysis for the Multi-Class Case with 3 Classes
s0 = 0.0048 (The 5 % quantile of the s values.)
Number of permutations: 90 (complete permutation)
MEAN number of falsely called genes is computed.
Delta p0 False Called FDR cutlow cutup
j2 j1
1 0.1 0.854 408.578 426 0.819 -Inf 16.599
0 12063
2 259.8 0.854 4.400 14 0.268 -Inf 483.139
0 12475
3 519.5 0.854 1.733 6 0.247 -Inf 786.998
0 12483
4 779.2 0.854 0.722 3 0.205 -Inf 1185.619
0 12486
5 1038.9 0.854 0.333 2 0.142 -Inf 2180.387
0 12487
6 1298.6 0.854 0.333 2 0.142 -Inf 2180.387
0 12487
7 1558.3 0.854 0.333 2 0.142 -Inf 2180.387
0 12487
8 1818.0 0.854 0.111 1 0.095 -Inf 3254.402
0 12488
9 2077.7 0.854 0.111 1 0.095 -Inf 3254.402
0 12488
10 2337.5 0.854 0.000 0 0.000 -Inf Inf
0 12489
Thank you so much in advance,
Saurin
