[BioC] Please Help with Starr Package

[Noah Dowell]

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