dear all, recently I tried old scripts running siggenes function. to have reproducibility with sam in excel I used the option lambda=0.5. now it seems that with siggenes 1.20.0 this option is not available. did it simply changed the name, or it was removed? furthermore if I run the summary I am not conviced by the FDR calculation. as you can see, using a minimum FC of 1.1, and a delta of 0.1, I have a FDR of 0.0141 but if I calculate the ratio between False Called genes and Called Genes, I have much higher FDR. this does not happen if I dont require any minimum FC summary(sam.H1vsCriF11) SAM Analysis for the Two-Class Unpaired Case Assuming Unequal Variances Number of variables having a fold change >= 1.1 or <= 0.9091 : 2098 s0 = 0 Number of permutations: 6 (complete permutation) MEDIAN number of falsely called variables is computed. Delta p0 False Called FDR cutlow cutup j2 j1 1 0.1 0.015 1922 2071 0.0141 -0.244 0.361 1022 1050 2 5.4 0.015 0 28 0 -11.876 11.812 13 2084 sessionInfo() R version 2.10.0 (2009-10-26) i686-pc-linux-gnu locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] tools splines stats graphics grDevices utils datasets [8] methods base other attached packages: [1] hgu133a.db_2.3.5 org.Hs.eg.db_2.3.6 annaffy_1.18.0 [4] KEGG.db_2.3.5 GO.db_2.3.5 hgu133acdf_2.5.0 [7] siggenes_1.20.0 multtest_2.2.0 limma_3.2.1 [10] lumi_1.12.2 MASS_7.3-3 RSQLite_0.7-3 [13] DBI_0.2-4 preprocessCore_1.8.0 mgcv_1.5-6 [16] annotate_1.20.1 xtable_1.5-6 AnnotationDbi_1.8.1 [19] gcrma_2.18.0 affy_1.24.2 Biobase_2.6.1 loaded via a namespace (and not attached): [1] affyio_1.14.0 Biostrings_2.14.8 grid_2.10.0 IRanges_1.4.9 [5] lattice_0.17-26 nlme_3.1-96 survival_2.35-7 [[alternative HTML version deleted]]