Hello To All, The early processing and normalization functions within Starr all seem to be working quite nicely so I quite grateful for this package, but I have stumbled in the graphing of the Affymetrix tiling array data. The vignette for the package has a nice example of plotting data in relation to all gene TSS's which I am trying to replicate. To do this I need a GFF file that has genomic features such as "gene" or "TSS" , etc. (I am also interested in other features such as telomeres, centromeres so the transcriptAnno.gff in the example will be quite limited in utility.) How do I create such a file? What files do I need? Where can I obtain them? (goldenpath, SGD, etc.??) I found the writeGFF function that uses a CEL and bpmap file to make a GFF but as far as I can tell that does not have genomic feature annotation information. Thank you in advance for any help!! noah > sessionInfo() R version 2.10.0 (2009-10-26) i386-apple-darwin9.8.0 locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] grid stats graphics grDevices utils datasets methods base other attached packages: [1] Starr_1.2.0 affxparser_1.18.0 affy_1.24.0 Ringo_1.10.0 Matrix_0.999375-31 lattice_0.17-26 [7] limma_3.2.1 RColorBrewer_1.0-2 Biobase_2.6.0 loaded via a namespace (and not attached): [1] affyio_1.14.0 annotate_1.24.0 AnnotationDbi_1.8.0 DBI_0.2-4 genefilter_1.28.0 [6] MASS_7.3-3 preprocessCore_1.8.0 pspline_1.0-13 RSQLite_0.7-3 splines_2.10.0 [11] survival_2.35-7 xtable_1.5-5

Noah Dowell wrote: > Hello To All, > > The early processing and normalization functions within Starr all seem to be working quite nicely so I quite grateful for this package, but I have stumbled in the graphing of the Affymetrix tiling array data. > > The vignette for the package has a nice example of plotting data in relation to all gene TSS's which I am trying to replicate. To do this I need a GFF file that has genomic features such as "gene" or "TSS" , etc. (I am also interested in other features such as telomeres, centromeres so the transcriptAnno.gff in the example will be quite limited in utility.) > > > > How do I create such a file? What files do I need? Where can I obtain them? (goldenpath, SGD, etc.??) Hi Noah -- One might get this info from a variety of sources, biomaRt::getBM being one rich possibility. Aim to create the gff with rtracklayer::export. library(biomaRt) listMart() listDatasets(useMart("fungal_mart_3")) mart = useMart("fungal_mart_3", "scerevisiae_eg_gene") listAttributes(mart) being a start. Martin > > > > > I found the writeGFF function that uses a CEL and bpmap file to make a GFF but as far as I can tell that does not have genomic feature annotation information. > > Thank you in advance for any help!! > > noah > > > >> sessionInfo() > R version 2.10.0 (2009-10-26) > i386-apple-darwin9.8.0 > > locale: > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] grid stats graphics grDevices utils datasets methods base > > other attached packages: > [1] Starr_1.2.0 affxparser_1.18.0 affy_1.24.0 Ringo_1.10.0 Matrix_0.999375-31 lattice_0.17-26 > [7] limma_3.2.1 RColorBrewer_1.0-2 Biobase_2.6.0 > > loaded via a namespace (and not attached): > [1] affyio_1.14.0 annotate_1.24.0 AnnotationDbi_1.8.0 DBI_0.2-4 genefilter_1.28.0 > [6] MASS_7.3-3 preprocessCore_1.8.0 pspline_1.0-13 RSQLite_0.7-3 splines_2.10.0 > [11] survival_2.35-7 xtable_1.5-5 > > _______________________________________________ > 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 -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793