Rob Dunne wrote: > Hi Benilton, > > yes, version 1.5.2 (and an upgrade of oligo and oligoClasses) fixed the > problem. > However the function "readPgfEnv" is not found Did you upgrade to R-devel, or simply install the devel version of pdInfoBuilder in your R-2.6.2 installation? > > Bye > Rob > > > > library(pdInfoBuilder) > pgfFile <- "RaGene-1_0-st-v1.r3.pgf" > clfFile <- "RaGene-1_0-st-v1.r3.clf" > transFile <- " RaGene-1_0-st-v1.na25.rn4.transcript.csv" > probeFile <- "RaGene-1_0-st-v1.probe.tab" > pkg <- new("AffyGenePDInfoPkgSeed", author = "Rob Dunne", email = > "rob.dunne at csiro.au", version = "0.0.1", genomebuild = "Fri Sep 26 > 19:30:54 2008", > biocViews = "AnnotationData", pgfFile = pgfFile, clfFile = clfFile, > transFile = transFile, probeFile = probeFile) > makePdInfoPackage(pkg) > #Error in chipName(object) : could not find function "readPgfEnv" > > > > Benilton Carvalho wrote: >> If you could, please, try version 1.5.2 (devel) and report back with >> your findings, I'd very much appreciate. >> >> http://www.bioconductor.org/packages/2.3/bioc/html/pdInfoBuilder.html >> >> best, >> >> b >> >> On Sep 28, 2008, at 9:48 PM, Rob Dunne wrote: >> >>> HI List, >>> I get the error message >>> >>> "AffyGenePDInfoPkgSeed" is not a defined class >>> >>> when I try to use pdInfoBuilder, but this posted example seems to >>> indicate it works for some. >>> >>> James W. MacDonald wrote: >>> >>>> You then have to create a 'AffyGenePDInfoPkgSeed' object which you can >>>> then use to build the package. The help page for this doesn't really >>>> cover this sort of thing, so here is an example of how you would do so: >>>> >>>> pgfFile <- "MoGene-1_0-st-v1.r3.pgf" >>>> clfFile <- "MoGene-1_0-st-v1.r3.clf" >>>> transFile <- "MoGene-1_0-st-v1.na24.mm8.transcript.csv" >>>> probeFile <- "MoGene-1_0-st-v1.probe.tab" >>>> >>>> pkg <- new("AffyGenePDInfoPkgSeed", author = "authorname", email = >>>> "e at mail.net", version = "0.0.1", genomebuild = "thegenomebuilddate", >>>> biocViews = "AnnotationData", pgfFile = pgfFile, clfFile = clfFile, >>>> transFile = transFile, probeFile = probeFile) >>>> >>>> makePdInfoPackage(pkg) >>> >>> library(pdInfoBuilder) >>> pgfFile <- "RaGene-1_0-st-v1.r3.pgf" >>> clfFile <- "RaGene-1_0-st-v1.r3.clf" >>> transFile <- " RaGene-1_0-st-v1.na25.rn4.transcript.csv" >>> probeFile <- "RaGene-1_0-st-v1.probe.tab" >>> >>> >>> >>> pkg <- new("AffyGenePDInfoPkgSeed", author = "Rob Dunne", email = >>> "rob.dunne at csiro.au", version = "0.0.1", genomebuild = "Fri Sep 26 >>> 19:30:54 2008", >>> biocViews = "AnnotationData", pgfFile = pgfFile, clfFile = clfFile, >>> transFile = transFile, probeFile = probeFile) >>> #Error in getClass(Class, where = topenv(parent.frame())) : >>> # "AffyGenePDInfoPkgSeed" is not a defined class >>> >>> pdInfoBuilder is the current version (1.2.0) and R is 2.6.2 >>> >>> Bye >>> Rob >>> >>> _______________________________________________ >>> 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 >> > > -- James W. MacDonald, M.S. Biostatistician Hildebrandt Lab 8220D MSRB III 1150 W. Medical Center Drive Ann Arbor MI 48109-0646 734-936-8662