Hi to all, I'm using sam function in siggenes package. Everything seems to be perfect. But when I try to summarize the results (for example, running the siggenes vignette) I'm not able to access directly the slots with the results. In the help file if I'm not wrong is written that the ouput of the sam function has to be a list, with specified slot... How I can access them ? (first: I found some output differences with the siggenes vignette...there, in the vignette, slots are reported in the output). Here's what I obtain running the vignette (BioC 1.6, R 2.1.0, WinXP): >sam.out <- sam(golub, golub.cl, rand = 123, gene.names = golub.gnames[, 3]) >summary(sam.out) SAM Analysis for the Two-Class Unpaired Case Assuming Unequal Variances s0 = 0.0584 (The 0 % quantile of the s values.) Number of permutations: 100 MEAN number of falsely called genes is computed. Delta p0 False Called FDR cutlow cutup j2 j1 1 0.1 0.5 2424.77 2739 0.443 -0.177 0.228 1434 1747 2 0.7 0.5 262.21 1248 0.105 -1.264 1.438 737 2541 3 1.3 0.5 12.11 507 0.012 -2.299 2.488 311 2856 4 1.8 0.5 0.74 210 0.002 -3.154 3.311 134 2976 5 2.4 0.5 0.01 76 0.000 -4.157 4.259 44 3020 6 3.0 0.5 0.00 15 0.000 -5.577 5.139 4 3041 7 3.6 0.5 0.00 5 0.000 -Inf 5.971 0 3047 8 4.1 0.5 0.00 2 0.000 -Inf 7.965 0 3050 9 4.7 0.5 0.00 2 0.000 -Inf 7.965 0 3050 10 5.3 0.5 0.00 0 0.000 -Inf Inf 0 3052 > That looks perfect. But, for example, the siggenes vignette says: "the general information about the set of significant genes [can be obtained] by >sum.sam.out$mat.fdr NULL " That's what I have: NULL ??? And the same is for all the specified (in the help file) slots... How can I have the FC list, the gene names, and all the results I need to continue my analysis? Where are the slots ? Well, what I'm doing wrong ? Any help will be appreciated !!!! Thanks a lot Giulio