[BioC] Can SAM be combined with the bootstrap with replacement method?

[Baskaran [guest]]

Hello,

I have a set of differentially expressed genes (DEG) mined from microarray data using the two-sample t-test with bootstrapping performed with replacement. 

I wanted to test the SAM method (using either the samr or siggenes package) for the detection of these DEG. However, the SAM method performs the selection of DEG with a permutation method, which I understand to be bootstrapping without replacement. As this method is intrinsic to SAM, I cannot change it.

I would like to run SAM on the microarray data combined with bootstrap with replacement, so that I can compare the results with my original t-test analysis a bit more clearly. 

Does anyone know of any package or method that can perform this step?

 -- output of sessionInfo(): 

R version 2.11.1 (2010-05-31) 
x86_64-pc-mingw32 

locale:
[1] LC_COLLATE=English_Singapore.1252  LC_CTYPE=English_Singapore.1252   
[3] LC_MONETARY=English_Singapore.1252 LC_NUMERIC=C                      
[5] LC_TIME=English_Singapore.1252    

attached base packages:
[1] splines   stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] samr_1.28       impute_1.22.0   siggenes_1.22.0 multtest_2.5.14 Biobase_2.8.0  

loaded via a namespace (and not attached):
[1] MASS_7.3-6      survival_2.35-8 tools_2.11.1

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