To all- I have finally figured out how to use ebam and incorparate a database so I can know what genes are interesting, or at least it was working yesterday but no longer. For some reason the ebam is not the right S4 object though I am using the same code as I did yesterday. I can not figure out where the issue is, hopefully someone else's keen eyes can spot where it has gone wrong. Sincerely Louisa YESTERDAYS Code > library(siggenes) Loading required package: multtest > Filter.mas <- exprs(Cum.mas.filter) > find.out <- find.a0(Filter.mas, cl, B=5000, rand=123456) We're doing 12870 complete permutations and randomly select 5000 of them. > ebam.out <- ebam(find.out) > ebam2excel(ebam.out, delta=0.9,file="Cumulus.csv", n.digits=4, what="both", quote=FALSE) Output is stored in Cumulus.csv > genenames <- list.siggenes(ebam.out, 0.9) > save.image("C:\\Documents and Settings\\Louisa Rispoli\\My Documents\\Louisa\\Rebecca Payton\\HS Microarray\\Cumulus Data\\Cumulus.Rdata") > library(bovine.db) Loading required package: AnnotationDbi Loading required package: DBI Loading required package: RSQLite > library(annaffy) Loading required package: GO.db Loading required package: KEGG.db > aaf.handler() [1] "Probe" "Symbol" "Description" "Chromosome" "Chromosome Location" [6] "GenBank" "Gene" "Cytoband" "UniGene" "PubMed" [11] "Gene Ontology" "Pathway" > anncols <- aaf.handler()[c(1:3, 6:7,11:12)] > anncols [1] "Probe" "Symbol" "Description" "GenBank" "Gene" "Gene Ontology" "Pathway" > anntable <- aafTableAnn(genenames, "bovine.db", anncols) > saveHTML(anntable, "Cumulus5000.html", title="Cumulus Data with 5000 permutations") > sessionInfo() R version 2.7.1 (2008-06-23) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] tcltk splines tools stats graphics grDevices utils datasets methods base other attached packages: [1] siggenes_1.14.0 multtest_1.20.0 affycoretools_1.12.1 annaffy_1.12.1 KEGG.db_2.2.0 biomaRt_1.14.0 [7] RCurl_0.9-3 GOstats_2.6.0 Category_2.6.0 RBGL_1.16.0 annotate_1.18.0 xtable_1.5-2 [13] GO.db_2.2.0 AnnotationDbi_1.2.2 RSQLite_0.6-9 DBI_0.2-4 graph_1.18.1 limma_2.14.5 [19] bovinecdf_2.2.0 tkWidgets_1.18.0 DynDoc_1.18.0 widgetTools_1.16.0 simpleaffy_2.16.0 gcrma_2.12.1 [25] matchprobes_1.12.0 genefilter_1.20.0 survival_2.34-1 affy_1.18.2 preprocessCore_1.2.1 affyio_1.8.1 [31] Biobase_2.0.1 loaded via a namespace (and not attached): [1] cluster_1.11.11 XML_1.94-0.1 TODAY'S CODE > library(siggenes) Loading required package: multtest > Filter.mas <- exprs(Cum.mas.filter) > find.out <- find.a0(Filter.mas, cl, B=5000, rand=123456) We're doing 12870 complete permutations and randomly select 5000 of them. > ebamCum <- ebam(find.out) > ebamCum EBAM Analysis for the Two-Class Unpaired Case Assuming Unequal Variances Fudge Factor: a0 = 0.0941 Delta Number FDR 1 0.9 77 0.0619 > CumNames <- list.siggenes(ebamCum, 0.9) Error in list.siggenes(ebamCum, 0.9) : no slot of name "row.sig.genes" for this object of class "table" In addition: Warning message: In list.siggenes(ebamCum, 0.9) : trying to get slot "row.sig.genes" from an object (class "table") that is not an S4 object > summary(ebamCum, 0.9) EBAM Analysis for the Two-Class Unpaired Case Assuming Unequal Variances Delta: 0.9 a0: 0.0941 p0: 1 Cutlow: -2.7031 Cutup: 2.4761 Identified Genes: 77 Estimated FDR: 0.06191 Identified Genes (posterior >= 0.9): Row z.value posterior local.fdr Name 1 6191 -4.160 0.9906 0.009395 Bt.26365.1.A1_at 2 5431 4.012 0.9909 0.009117 Bt.24179.1.A1_at 3 9987 3.917 0.9894 0.010574 Bt.8479.1.A1_at 4 8305 -3.857 0.9845 0.015473 Bt.4714.1.S1_at 5 6083 -3.714 0.9804 0.019568 Bt.2577.1.S1_at 6 4100 -3.567 0.9751 0.024895 Bt.21220.1.S1_at 7 3314 3.563 0.9816 0.018380 Bt.19889.1.A1_at 8 3986 3.523 0.9804 0.019572 Bt.20994.1.S1_at 9 7822 3.497 0.9796 0.020381 Bt.3797.1.S1_at 10 9166 -3.387 0.9666 0.033366 Bt.6438.1.A1_at 11 1573 -3.381 0.9663 0.033686 Bt.13993.2.S1_at 12 3759 3.366 0.9750 0.024994 Bt.20520.1.S1_at 13 1572 -3.289 0.9609 0.039091 Bt.13993.1.A1_at 14 7051 3.274 0.9712 0.028841 Bt.28332.1.S1_at 15 9507 3.265 0.9708 0.029246 Bt.7190.1.S1_at 16 4671 -3.264 0.9593 0.040720 Bt.2230.1.S2_at > ebam2excel(ebamCum, delta=0.9,file="Cumulus.csv", n.digits=4, what="both", quote=FALSE) Length Class Mode 1 EBAM S4 R version 2.7.1 (2008-06-23) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] tcltk splines tools stats graphics grDevices utils datasets methods base other attached packages: [1] siggenes_1.14.0 multtest_1.20.0 affycoretools_1.12.1 annaffy_1.12.1 KEGG.db_2.2.0 biomaRt_1.14.0 [7] RCurl_0.9-3 GOstats_2.6.0 Category_2.6.0 RBGL_1.16.0 annotate_1.18.0 xtable_1.5-2 [13] GO.db_2.2.0 AnnotationDbi_1.2.2 RSQLite_0.6-9 DBI_0.2-4 graph_1.18.1 limma_2.14.5 [19] bovinecdf_2.2.0 tkWidgets_1.18.0 DynDoc_1.18.0 widgetTools_1.16.0 simpleaffy_2.16.0 gcrma_2.12.1 [25] matchprobes_1.12.0 genefilter_1.20.0 survival_2.34-1 affy_1.18.2 preprocessCore_1.2.1 affyio_1.8.1 [31] Biobase_2.0.1 loaded via a namespace (and not attached): [1] cluster_1.11.11 XML_1.94-0.1 "If we knew what we were doing, it wouldn't be called Research." - Albert Einstein Louisa Rispoli, Ph.D. Reproductive Physiology Department of Animal Science University of Tennessee, Knoxville A105 Johnson Animal Research and Teaching Unit 1750 Alcoa Highway Knoxville, TN 37920 phone:(865) 946-1874 fax:(865) 946-1010 email: lrispoli at utk.edu