Please Help with Starr Package
1
0
Entering edit mode
Noah Dowell ▴ 410
@noah-dowell-3791
Last seen 7.1 years ago
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
Normalization Starr Normalization Starr • 542 views
ADD COMMENT
0
Entering edit mode
@martin-morgan-1513
Last seen 3 months ago
United States
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
ADD COMMENT

Login before adding your answer.

Traffic: 231 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6