Hello, I am running SPIA (downloaded from the Bioconductor source repository 8/5/2010) on Affymetrix MoGene data collected for mouse using the following command: res = spia(de = DE, all = ALL, organism = "mmu", nB = 2000, plots = FALSE, beta = NULL) The procedure runs to completion and produces results and shows several pathways with significant perturbation, but the pSize and NDE are always equal for every pathway evaluated - the top 10 are listed below. Name ID pSize NDE tA pNDE pPERT 1 Cytokine-cytokine receptor int 04060 44 44 17.81364905 1 0.000005 2 Chemokine signaling pathway 04062 44 44 70.55024083 1 0.000005 3 Antigen processing and present 04612 19 19 19.20487487 1 0.000005 4 Intestinal immune network for 04672 17 17 11.53587339 1 0.000005 5 Olfactory transduction 04740 43 43 -45.40999859 1 0.000005 6 Type I diabetes mellitus 04940 13 13 17.52273370 1 0.000005 7 Autoimmune thyroid disease 05320 13 13 17.48652443 1 0.000005 8 Systemic lupus erythematosus 05322 28 28 21.08154901 1 0.000005 9 Allograft rejection 05330 14 14 17.65594344 1 0.000005 10 Graft-versus-host disease 05332 12 12 17.59478491 1 0.000005 This must be an error - Any thoughts on why I might see this? Thanks! Will ______________________________ William S. Bush, PhD, MS Assistant Professor Center for Human Genetics Research Department of Biomedical Informatics Vanderbilt University Nashville, TN 37232 [[alternative HTML version deleted]]