Hello, I observed the following problem when using the KEGG annotation with hyperGTest: Somehow hyperGTest does not consider all genes. In the example below, all three genes are in the category "05020" (this is what mget(genes,envir=org.Hs.egPATH) says). In the summary of hyperGTest, however, the category contains only two genes. Is there an explanation of this behavior? Thanks in advance! Anne > library("Category") Loading required package: AnnotationDbi Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. > library("org.Hs.eg.db") Loading required package: DBI > genes=c("1958","3553","3303") > > GoHyp=new("KEGGHyperGParams",geneIds=genes,annotation="org.Hs.eg",pval ueCutoff=1,testDirection="over") > htest=hyperGTest(GoHyp) > s=summary(htest) > s[1,] KEGGID Pvalue OddsRatio ExpCount Count Size Term 1 05020 3.810228e-06 Inf 0.003960844 2 35 Prion diseases > > p=mget(genes,envir=org.Hs.egPATH,ifnotfound=NA) > p $`1958` [1] "05020" $`3553` [1] "04010" "04060" "04210" "04620" "04640" "04940" "05010" "05020" "05332" $`3303` [1] "04010" "04144" "04612" "05020" > geneIdsByCategory(htest,"05020") $`05020` [1] "1958" "3553" > sessionInfo() R version 2.10.0 (2009-10-26) x86_64-unknown-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] stats graphics grDevices utils datasets methods base other attached packages: [1] KEGG.db_2.3.5 org.Hs.eg.db_2.3.6 RSQLite_0.7-3 [4] DBI_0.2-4 Category_2.12.0 AnnotationDbi_1.8.1 [7] Biobase_2.6.0 loaded via a namespace (and not attached): [1] annotate_1.24.0 genefilter_1.28.0 graph_1.24.1 GSEABase_1.8.0 [5] RBGL_1.22.0 splines_2.10.0 survival_2.35-7 tools_2.10.0 [9] XML_2.6-0 xtable_1.5-6 >

Hi Anne, Unfortunately, this is a small bug you have uncovered that can affect people using Category to do KEGG analysis. I have just fixed it, and a patched version should be available within a day or so via biocLite(). Good job on finding that, and thanks for sharing. Marc On 04/14/2010 08:04 AM, Anne Kupczok wrote: > Hello, > I observed the following problem when using the KEGG annotation with > hyperGTest: Somehow hyperGTest does not consider all genes. In the > example below, all three genes are in the category "05020" (this is > what mget(genes,envir=org.Hs.egPATH) says). In the summary of > hyperGTest, however, the category contains only two genes. > Is there an explanation of this behavior? > Thanks in advance! > Anne > > > library("Category") > Loading required package: AnnotationDbi > Loading required package: Biobase > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > 'openVignette()'. To cite Bioconductor, see > 'citation("Biobase")' and for packages 'citation(pkgname)'. > > > library("org.Hs.eg.db") > Loading required package: DBI > > genes=c("1958","3553","3303") > > > > > GoHyp=new("KEGGHyperGParams",geneIds=genes,annotation="org.Hs.eg",pv alueCutoff=1,testDirection="over") > > > htest=hyperGTest(GoHyp) > > s=summary(htest) > > s[1,] > KEGGID Pvalue OddsRatio ExpCount Count Size Term > 1 05020 3.810228e-06 Inf 0.003960844 2 35 Prion diseases > > > > p=mget(genes,envir=org.Hs.egPATH,ifnotfound=NA) > > p > $`1958` > [1] "05020" > > $`3553` > [1] "04010" "04060" "04210" "04620" "04640" "04940" "05010" "05020" > "05332" > > $`3303` > [1] "04010" "04144" "04612" "05020" > > > geneIdsByCategory(htest,"05020") > $`05020` > [1] "1958" "3553" > > > sessionInfo() > R version 2.10.0 (2009-10-26) > x86_64-unknown-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] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] KEGG.db_2.3.5 org.Hs.eg.db_2.3.6 RSQLite_0.7-3 > [4] DBI_0.2-4 Category_2.12.0 AnnotationDbi_1.8.1 > [7] Biobase_2.6.0 > > loaded via a namespace (and not attached): > [1] annotate_1.24.0 genefilter_1.28.0 graph_1.24.1 GSEABase_1.8.0 > [5] RBGL_1.22.0 splines_2.10.0 survival_2.35-7 tools_2.10.0 > [9] XML_2.6-0 xtable_1.5-6 > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >