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

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