Thank you. Your reply helps a lot in letting me know where to look for things. :) Best, G On Wed, Aug 27, 2014 at 11:08 AM, James W. MacDonald <jmacdon at="" uw.edu=""> wrote: > Hi Guilherme, > > > On Tue, Aug 26, 2014 at 10:00 AM, Guilherme Rocha <gvrocha at="" gmail.com=""> > wrote: > >> Hi all, >> >> I have constructed a package information file for Affy's HTA 2.0 chip >> using pdInfoBuilder as shown below. >> It appears that the annotation files have been upgraded to na34 (from >> na33 in probeFile and transFile). >> >> Specific question: do the annotation files affect which probes are >> included in each probeset/trascript cluster? >> > > They can. It depends on changes between the current genome build and the > one on which the original probeset/transcript clusters were based. Given > the maturity of the Human Genome, I wouldn't expect massive changes. > > >> Broader question: what information from the annotation files is actually >> used by pdInfoBuider? >> > > This is something you could explore for yourself. If you go to the svn ( > https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks), using > readonly for both the password and user name, and look at the source for > pdBuilderV2HTA2.R, you can see this near the top, in the function > parseHtaProbesetCSV(): > > > cols <- c("probeset_id", "seqname", "strand", "start", "stop", > "transcript_cluster_id", "exon_id", > "crosshyb_type", "level", "probeset_type", > "junction_start_edge", "junction_stop_edge", > "junction_sequence", "has_cds") > > So all of this information is parsed out of the probeset CSV file. If > there are changes to the current human genome that would imply that a > particular probe or probeset no longer measures what Affy originally > intended (or if the strand, start, or stop position change), then the > changes would be reflected here, and would then be passed to the pd.hta.2.0 > package that you built. > > The transcript CSV file is used for much less. AFAIK, that file is just > parsed and put into the extdata directory of the package: > > > #################################################################### ### > ## Part vi) Save NetAffx Annotation to extdata > > #################################################################### ### > if (!quiet) message("Saving NetAffx Annotation... ", > appendLF=FALSE) > netaffxProbeset <- annot2fdata(object at probeFile) > save(netaffxProbeset, file=file.path(extdataDir, > 'netaffxProbeset.rda'), compress='xz') > netaffxTranscript <- annot2fdata(object at transFile) > save(netaffxTranscript, file=file.path(extdataDir, > 'netaffxTranscript.rda'), > compress='xz') > > And you can see what that looks like by doing: > > load(paste0(path.package("pd.hta.2.0"), "/extdata/netaffxTranscript.rda")) > > and then > > head(pData(netaffxTranscript)) > > but I don't think these data are currently used for anything. > > Best, > > Jim > > > > >> >> Any help appreciated. >> >> Thanks, >> >> Guilherme Rocha >> >> >> >> ------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------- >> Construction fo the package: >> >> library(pdInfoBuilder) >> >> setwd("/my_bioc_packages/") >> >> seed <- new("AffyHTAPDInfoPkgSeed", >> version = "3.8.0", >> license = "Artistic-2.0", >> pgfFile = ".../HTA-2_0.r1.pgf", >> clfFile = ".../HTA-2_0.r1.clf", >> probeFile = ".../HTA-2_0.na33.hg19.probeset.csv", >> transFile = ".../HTA-2_0.na33.1.hg19.transcript.csv", >> coreMps = ".../HTA-2_0.r1.Psrs.mps", >> geneArray = TRUE, >> author = "gvrocha", >> email = "gvrocha at gmail.com", >> biocViews = "AnnotationData", >> genomebuild = "hg19", >> organism = "Homo sapiens", >> species = "Homo sapien", >> url = "http://about.me/gvrocha") >> >> makePdInfoPackage(seed, destDir=".") >> >> >> -- >> Guilherme V. Rocha >> gvrocha at gmail.com >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > -- Guilherme V. Rocha gvrocha at gmail.com [[alternative HTML version deleted]]