Hello,
I am using the package siggenes for multiclass problem.
 (R 2.6.0 ;BioConductor 2.1;siggenes 1.2.11)
My dataset is 9 samples in 3 classes, each class contains 3 samples.
There are totally 13915 genes.
When I using siggenes to do Multiclass SAM,
(code:   samResults<-sam(dd,cl, B=500, rand=123) )
the results are as follow:

SAM Analysis for the Multi-Class Case with 3 Classes

    Delta    p0     False     Called      FDR
1     0.1 0.061     11893.018 13745       0.052440
2   913.6 0.061     0.538     59          0.000553
3  1827.2 0.061     0.084     12          0.000424

Also,I know I can use SAM for EXCEL to do this.
However, the results are quite different:

delta	# med false pos	90th perc false pos # called	median FDR	90th perc FDR	

0.099   2119.652318	2173.516349	      13863	0.152899972	0.156785425	
1.046	110.2554078	341.349479            10251	0.010755576	0.033299139	
7.156	0	        3.475098814	      1166	0	        0.002980359	
14.86	0               0.473877111	      166	0	        0.002854681	
61.90	0	        0	              1	        0	        0	

Both of them are computed with 500 permutation, and rand seed 123.
What's going wrong with my work?

I have read manual for several times(siggenes.pdf),
but the only information about multiclass is how to assign grouping.
Should I assign more parameters when using SAM? How?

Thank you very much for answering.


Sincerely,
Ruo Yang, Lu


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