Robert, thanks for the point in the right direction. Chips I have used previously have already had these packages built and the process has been opaque to me. Mark ------------------------------------------------------------ Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 399-1219 Home Skype: mkimpel "The real problem is not whether machines think but whether men do." -- B. F. Skinner ****************************************************************** On Mon, Oct 20, 2008 at 12:48 PM, Robert Gentleman <rgentlem@fhcrc.org>wrote: > Mark, > Category requires annotation packages, not cdfs. I am not sure why you > think information on where a probe is located on the chip would be useful > for a GSEA analysis, but if there is something in the docs, please let me > know. > > You can use AnnotationDbi to build an annotation package for that chip, if > one does not exist. Please see the vignette etc. > > best wishes > Robert > > > Mark Kimpel wrote: > >> I have built a package with makecdf using files supplied by Affy for their >> Rat Gene ST array. It does not seem to work with the Category package as >> it >> does not seem to have GO information incorporated. Output with some >> debugging info is below. Far below is the script I used to generate the >> Gene >> ST package. >> >> [1] "beginning Category analysis" >> Loading required package: ragene10stv1.cdf.db >> Error in get(mapName, envir = pkgEnv, inherits = FALSE) : >> variable "ragene10stv1.cdfGO" was not found >> >> Enter a frame number, or 0 to exit >> >> 1: limma.contrast.output.func(AOP, fit2, rslt, contrast.num = 1, >> custom.contra >> 2: category.wrapper.func(CatToTest = "ALL", FC.dir = "all", input.df = >> t.tab.a >> 3: Cat.anal.func(CatToTest[i], input.df, FC.dir, annotationPckg, >> entrez.univer >> 4: CatHyperMaxCats.func(CatToTest, optimizedParam) >> 5: hyperGTest(params) >> 6: .valueClassTest(standardGeneric("hyperGTest"), "HyperGResultBase", >> "hyperGT >> 7: is(object, Cl) >> 8: is(object, Cl) >> 9: universeBuilder(p) >> 10: universeBuilder(p) >> 11: getUniverseViaGo(p) >> 12: eapply(ID2GO(datPkg), function(goids) { >> 13: ID2GO(datPkg) >> 14: ID2GO(datPkg) >> 15: getAnnMap("GO", p@name) >> 16: get(mapName, envir = pkgEnv, inherits = FALSE) >> 17: get(mapName, envir = pkgEnv, inherits = FALSE) >> >> Selection: 17 >> Called from: eval(expr, envir, enclos) >> Browse[1]> ls() >> [1] "envir" "inherits" "mode" "pos" "x" >> Browse[1]> ls(envir) >> [1] "i2xy" "ragene10stv1.cdf" "ragene10stv1.dim" "xy2i" >> >> >> Browse[1]> sessionInfo() >> R version 2.8.0 beta (2008-10-10 r46685) >> 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;L C_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDE NTIFICATION=C >> >> attached base packages: >> [1] tcltk splines tools stats graphics grDevices utils >> [8] datasets methods base >> >> other attached packages: >> [1] ragene10stv1.cdf_1.19.0 qvalue_1.15.0 affycoretools_1.13.4 >> [4] annaffy_1.13.1 KEGG.db_2.2.5 gcrma_2.13.2 >> [7] matchprobes_1.13.1 biomaRt_1.15.4 GOstats_2.7.0 >> [10] Category_2.7.6 genefilter_1.21.5 survival_2.34-1 >> [13] RBGL_1.17.2 annotate_1.19.3 xtable_1.5-4 >> [16] GO.db_2.2.5 AnnotationDbi_1.3.12 RSQLite_0.7-0 >> [19] DBI_0.2-4 limma_2.15.16 affy_1.19.4 >> [22] preprocessCore_1.3.4 affyio_1.9.1 Biobase_2.1.7 >> [25] graph_1.19.6 >> >> loaded via a namespace (and not attached): >> [1] cluster_1.11.11 GSEABase_1.3.6 RCurl_0.91-0 XML_1.98-0 >> >> >> require(makecdfenv) >> setwd('~/R.functions/Annotation_builds/Rat_ST_1.0_lib_files') >> >> system('mv RaGene-1_0-st-v1.r3.cdf RaGene-1_0-st-v1.cdf') >> >> cdf.file <- "RaGene-1_0-st-v1.cdf" >> pckg.name <- substring(cleancdfname(cdf.file), 1, >> nchar(cleancdfname(cdf.file)) - 4, unlink = TRUE) >> make.cdf.package(cdf.file, species = "Rattus_nor", packagename=pckg.name) >> >> #followed by R CMD INSTALL of package >> ------------------------------------------------------------ >> Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry >> Indiana University School of Medicine >> >> 15032 Hunter Court, Westfield, IN 46074 >> >> (317) 490-5129 Work, & Mobile & VoiceMail >> (317) 399-1219 Home >> Skype: mkimpel >> >> "The real problem is not whether machines think but whether men do." -- B. >> F. Skinner >> ****************************************************************** >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> > -- > Robert Gentleman, PhD > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M2-B876 > PO Box 19024 > Seattle, Washington 98109-1024 > 206-667-7700 > rgentlem@fhcrc.org > [[alternative HTML version deleted]]