Hi all, I wanted to test for chromosomal region enriched for my list of DE genes. I tried with the ChrMapHyperGParams but it looks like that just Human and mice are supported (see below). I am really interested in this approach, and would like to know if it would be difficult to implement such support or there is any other package out there doing a similar job. If there is not a 'off the shelf' solution to this, the simplest possible question would be if my D.E. genes are enriched in sexual chromosomes vs. autosomes. Is there a better approach than a chisq.test? Thanks, paolo > temp.params <- new("ChrMapHyperGParams", + conditional=FALSE, + testDirection="over", + universeGeneIds=univ, + geneIds=id.int, + annotation=annotation(eset), + pvalueCutoff=0.05) > temp <- hyperGTest(temp.params) Error: 'ORGANISM:Drosophila melanogaster' is not a supported. organism must be one of: ORGANISM:Homo sapiens, ORGANISM:Mus musculus > sessionInfo() R version 2.9.0 (2009-04-17) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] GOstats_2.10.0 graph_1.22.2 Category_2.10.0 [4] drosophila2.db_2.2.11 annaffy_1.16.0 affycoretools_1.16.0 [7] KEGG.db_2.2.11 GO.db_2.2.11 AnnotationDbi_1.6.0 [10] affy_1.22.0 Biobase_2.4.1 RSQLite_0.7-1 [13] DBI_0.2-4 loaded via a namespace (and not attached): [1] affyio_1.12.0 annotate_1.22.0 biomaRt_2.0.0 [4] gcrma_2.16.0 genefilter_1.24.0 grid_2.9.0 [7] GSEABase_1.6.0 lattice_0.17-22 limma_2.18.0 [10] lme4_0.999375-28 Matrix_0.999375-26 MCMCglmm_1.09 [13] preprocessCore_1.6.0 RBGL_1.20.0 RCurl_0.94-1 [16] splines_2.9.0 survival_2.35-4 tools_2.9.0 [19] XML_2.3-0 xtable_1.5-5 -- Paolo Innocenti Department of Animal Ecology, EBC Uppsala University Norbyv?gen 18D 75236 Uppsala, Sweden

Hi Paolo, We already provide basic chromosome band information for flies. Therefore, it should be completely possible to just make adjustments to the Category package to make this work. However, the tricky part is that human, mouse and fly all record such data is a slightly different style of notation. And so for supported organisms some extra functionality would have to be added to Category in order to deal with this. If you are interested you might want to have a look at MAPcode.R in the Category package. There should already be examples there for human and mouse. If you have the time and inclination to make this work, I would love to include your efforts so that everyone else can benefit. Marc Paolo Innocenti wrote: > Hi all, > > I wanted to test for chromosomal region enriched for my list of DE genes. > I tried with the ChrMapHyperGParams but it looks like that just Human > and mice are supported (see below). > > I am really interested in this approach, and would like to know if it > would be difficult to implement such support or there is any other > package out there doing a similar job. > > If there is not a 'off the shelf' solution to this, the simplest > possible question would be if my D.E. genes are enriched in sexual > chromosomes vs. autosomes. Is there a better approach than a chisq.test? > > Thanks, > paolo > > > temp.params <- new("ChrMapHyperGParams", > + conditional=FALSE, > + testDirection="over", > + universeGeneIds=univ, > + geneIds=id.int, > + annotation=annotation(eset), > + pvalueCutoff=0.05) > > temp <- hyperGTest(temp.params) > Error: 'ORGANISM:Drosophila melanogaster' is not a supported. > organism must be one of: ORGANISM:Homo sapiens, ORGANISM:Mus musculus > > sessionInfo() > R version 2.9.0 (2009-04-17) > x86_64-unknown-linux-gnu > > locale: > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_ US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC _NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDEN TIFICATION=C > > > attached base packages: > [1] stats graphics grDevices datasets utils methods base > > other attached packages: > [1] GOstats_2.10.0 graph_1.22.2 Category_2.10.0 > [4] drosophila2.db_2.2.11 annaffy_1.16.0 affycoretools_1.16.0 > [7] KEGG.db_2.2.11 GO.db_2.2.11 AnnotationDbi_1.6.0 > [10] affy_1.22.0 Biobase_2.4.1 RSQLite_0.7-1 > [13] DBI_0.2-4 > > loaded via a namespace (and not attached): > [1] affyio_1.12.0 annotate_1.22.0 biomaRt_2.0.0 > [4] gcrma_2.16.0 genefilter_1.24.0 grid_2.9.0 > [7] GSEABase_1.6.0 lattice_0.17-22 limma_2.18.0 > [10] lme4_0.999375-28 Matrix_0.999375-26 MCMCglmm_1.09 > [13] preprocessCore_1.6.0 RBGL_1.20.0 RCurl_0.94-1 > [16] splines_2.9.0 survival_2.35-4 tools_2.9.0 > [19] XML_2.3-0 xtable_1.5-5 >