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 -- Sent via the guest posting facility at bioconductor.org.