Question: inquiry for CDF file
0
gravatar for Rob Dunne
11.2 years ago by
Rob Dunne230
Rob Dunne230 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
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ADD COMMENTlink modified 11.2 years ago • written 11.2 years ago by Rob Dunne230
Answer: inquiry for CDF file
0
gravatar for Rob Dunne
11.2 years ago by
Rob Dunne230
Rob Dunne230 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 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 > -- Rob Dunne Fax: +61 2 9325 3200 Tel: +61 2 9325 3263 CSIRO Mathematical and Information Sciences +61 2 9325 3100 Locked Bag 17, North Ryde, New South Wales, Australia, 1670 http://www.bioinformatics.csiro.au Email: Rob.Dunne at csiro.au Java has certainly revolutionized marketing and litigation.
ADD COMMENTlink written 11.2 years ago by Rob Dunne230
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
ADD REPLYlink written 11.2 years ago by James W. MacDonald52k
James W. MacDonald wrote: > Did you upgrade to R-devel, or simply install the devel version of > pdInfoBuilder in your R-2.6.2 installation? > Hi James, I just installed the devel version of pdInfoBuilder in my R-2.6.2 installation. I have now installed R-devel and pdInfoBuilder is working as expected > makePdInfoPackage(pkg,destDir=".") Creating package in ./pd.ragene.1.0.st.v1 I guess I misunderstood what was required. Thanks Rob -- Rob Dunne Fax: +61 2 9325 3200 Tel: +61 2 9325 3263 CSIRO Mathematical and Information Sciences +61 2 9325 3100 Locked Bag 17, North Ryde, New South Wales, Australia, 1670 http://www.bioinformatics.csiro.au Email: Rob.Dunne at csiro.au Java has certainly revolutionized marketing and litigation.
ADD REPLYlink written 11.2 years ago by Rob Dunne230
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