Question: pdInfoBuilder: invalid class object ("ScalarCharacter")
0
gravatar for Guido Hooiveld
9.5 years ago by
Guido Hooiveld2.5k
Wageningen University, Wageningen, the Netherlands
Guido Hooiveld2.5k wrote:
Dear list, I am trying to build an annotation package for the Mouse Gene 1.1 ST Array Plate (GeneTitan peg array) using pdInfoBuilder. As input i use the PGF, CLF, etc files downloaded from Affymetrix. However, the following lines of code do not work; specifically I am puzzled by the error message that a file is in the wrong "format". Can someone please explain what this error means (i have never heard of 'ScalarCharacter'), and how to solve it? Thanks, Guido http://www.affymetrix.com/browse/products.jsp?productId=131555&navMode =3 4000&navAction=jump&aId=productsNav#1_3 > library("pdInfoBuilder") Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. Loading required package: RSQLite Loading required package: DBI Loading required package: affxparser Loading required package: oligo Loading required package: oligoClasses Loading required package: preprocessCore Welcome to oligo version 1.10.0 > > pgfFile = "MoGene-1_1-st-v1.r4.pgf"; > clfFile = "MoGene-1_1-st-v1.r4.clf"; > probeFile = "MoGene-1_1-st-v1.mm8.probe.tab"; > transFile = "MoGene-1_1-st-v1.na30.1.mm9.transcript.csv"; > pkg <- new("AffyGenePDInfoPkgSeed", + version="0.0.1", + author="Guido Hooiveld", email=guido.hooiveld@xxx, + biocViews="AnnotationData", + genomebuild="mm8", + pgfFile=pgfFile, clfFile=clfFile, + probeFile=probeFile, transFile=transFile); Error in validObject(.Object) : invalid class "AffyGenePDInfoPkgSeed" object: invalid object for slot "transFile" in class "AffyGenePDInfoPkgSeed": got class "character", should be or extend class "ScalarCharacter" > sessionInfo() R version 2.10.1 (2009-12-14) x86_64-unknown-linux-gnu locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] pdInfoBuilder_1.10.1 oligo_1.10.0 preprocessCore_1.8.0 [4] oligoClasses_1.8.0 affxparser_1.18.0 RSQLite_0.8-0 [7] DBI_0.2-5 Biobase_2.6.1 loaded via a namespace (and not attached): [1] affyio_1.14.0 Biostrings_2.14.10 IRanges_1.4.9 splines_2.10.1 [5] tools_2.10.1 ------------------------------------------------ Guido Hooiveld, PhD Nutrition, Metabolism & Genomics Group Division of Human Nutrition Wageningen University Biotechnion, Bomenweg 2 NL-6703 HD Wageningen the Netherlands tel: (+)31 317 485788 fax: (+)31 317 483342 internet: http://nutrigene.4t.com <http: nutrigene.4t.com=""/> email: guido.hooiveld@wur.nl [[alternative HTML version deleted]]
ADD COMMENTlink modified 9.5 years ago by Vincent J. Carey, Jr.6.3k • written 9.5 years ago by Guido Hooiveld2.5k
Answer: pdInfoBuilder: invalid class object ("ScalarCharacter")
0
gravatar for Seth Falcon
9.5 years ago by
Seth Falcon7.4k
Seth Falcon7.4k wrote:
On 4/7/10 11:55 AM, Hooiveld, Guido wrote: > Dear list, > I am trying to build an annotation package for the Mouse Gene 1.1 ST > Array Plate (GeneTitan peg array) using pdInfoBuilder. As input i use > the PGF, CLF, etc files downloaded from Affymetrix. However, the > following lines of code do not work; specifically I am puzzled by the > error message that a file is in the wrong "format". Can someone please > explain what this error means (i have never heard of 'ScalarCharacter'), > and how to solve it? > Thanks, > Guido > > http://www.affymetrix.com/browse/products.jsp?productId=131555&navMo de=3 > 4000&navAction=jump&aId=productsNav#1_3 > > >> library("pdInfoBuilder") > Loading required package: Biobase > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > 'openVignette()'. To cite Bioconductor, see > 'citation("Biobase")' and for packages 'citation(pkgname)'. > > Loading required package: RSQLite > Loading required package: DBI > Loading required package: affxparser > Loading required package: oligo > Loading required package: oligoClasses > Loading required package: preprocessCore > Welcome to oligo version 1.10.0 >> >> pgfFile = "MoGene-1_1-st-v1.r4.pgf"; >> clfFile = "MoGene-1_1-st-v1.r4.clf"; >> probeFile = "MoGene-1_1-st-v1.mm8.probe.tab"; >> transFile = "MoGene-1_1-st-v1.na30.1.mm9.transcript.csv"; >> pkg<- new("AffyGenePDInfoPkgSeed", > + version="0.0.1", > + author="Guido Hooiveld", email=guido.hooiveld at xxx, Perhaps it is that you are missing quotes around your email address?
ADD COMMENTlink written 9.5 years ago by Seth Falcon7.4k
Hi Seth, No, that is not the case. I noticed the missing quotes as well after sending the email, but that happened when I removed part of my email address (b/o spam). Thus, to confirm, these lines of code do not work: Guido > pkg <- new("AffyGenePDInfoPkgSeed", + version="0.0.1", + author="Guido Hooiveld", email="guido.hooiveld at xxx.nl", + biocViews="AnnotationData", + genomebuild="mm8", + pgfFile=pgfFile, clfFile=clfFile, + probeFile=probeFile, transFile=transFile); Error in validObject(.Object) : invalid class "AffyGenePDInfoPkgSeed" object: invalid object for slot "transFile" in class "AffyGenePDInfoPkgSeed": got class "character", should be or extend class "ScalarCharacter" > > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of > Seth Falcon > Sent: 07 April 2010 21:09 > To: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] pdInfoBuilder: invalid class object > ("ScalarCharacter") > > On 4/7/10 11:55 AM, Hooiveld, Guido wrote: > > Dear list, > > I am trying to build an annotation package for the Mouse > Gene 1.1 ST > > Array Plate (GeneTitan peg array) using pdInfoBuilder. As > input i use > > the PGF, CLF, etc files downloaded from Affymetrix. However, the > > following lines of code do not work; specifically I am > puzzled by the > > error message that a file is in the wrong "format". Can > someone please > > explain what this error means (i have never heard of > > 'ScalarCharacter'), and how to solve it? > > Thanks, > > Guido > > > > > http://www.affymetrix.com/browse/products.jsp?productId=131555&navMode > > =3 > > 4000&navAction=jump&aId=productsNav#1_3 > > > > > >> library("pdInfoBuilder") > > Loading required package: Biobase > > > > Welcome to Bioconductor > > > > Vignettes contain introductory material. To view, type > > 'openVignette()'. To cite Bioconductor, see > > 'citation("Biobase")' and for packages 'citation(pkgname)'. > > > > Loading required package: RSQLite > > Loading required package: DBI > > Loading required package: affxparser > > Loading required package: oligo > > Loading required package: oligoClasses Loading required package: > > preprocessCore Welcome to oligo version 1.10.0 > >> > >> pgfFile = "MoGene-1_1-st-v1.r4.pgf"; > >> clfFile = "MoGene-1_1-st-v1.r4.clf"; > >> probeFile = "MoGene-1_1-st-v1.mm8.probe.tab"; transFile = > >> "MoGene-1_1-st-v1.na30.1.mm9.transcript.csv"; > >> pkg<- new("AffyGenePDInfoPkgSeed", > > + version="0.0.1", > > + author="Guido Hooiveld", email=guido.hooiveld at xxx, > > Perhaps it is that you are missing quotes around your email address? > > _______________________________________________ > 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 > >
ADD REPLYlink written 9.5 years ago by Guido Hooiveld2.5k
Answer: pdInfoBuilder: invalid class object ("ScalarCharacter")
0
gravatar for Vincent J. Carey, Jr.
9.5 years ago by
United States
Vincent J. Carey, Jr.6.3k wrote:
This is not a message about a file format. It says that the input to the class definition for slot transFile is of the wrong class. Try transFile = new("ScalarCharacter", [your filename]) and see where you get. Note > getClass("AffyGenePDInfoPkgSeed") Class "AffyGenePDInfoPkgSeed" [package "pdInfoBuilder"] Slots: Name: pgfFile clfFile probeFile transFile Class: ScalarCharacter ScalarCharacter ScalarCharacter ScalarCharacter Name: coreMps fullMps extendedMps geneArray Class: ScalarCharacter ScalarCharacter ScalarCharacter logical Name: version license author email Class: character character character character Name: biocViews chipName manufacturer url Class: character character character character Name: genomebuild organism species Class: character character character Extends: Class "AffySTPDInfoPkgSeed", directly Class "AffymetrixPDInfoPkgSeed", by class "AffySTPDInfoPkgSeed", distance 2 Class "PDInfoPkgSeed", by class "AffySTPDInfoPkgSeed", distance 3 showing that some of the slots need to be instances of ScalarCharacter, others can be plain character. Furthermore > getClass("ScalarCharacter") Class "ScalarCharacter" [package "Biobase"] Slots: Name: .Data Class: character Extends: Class "ScalarObject", directly Class "character", from data part Class "vector", by class "character", distance 2 Class "data.frameRowLabels", by class "character", distance 2 Class "characterORMIAME", by class "character", distance 2 note furthermore > getValidity(getClass("ScalarObject")) function (object) { if (length(object) != 1L) paste(class(object), "must have length one") else TRUE } <environment: namespace:biobase=""> On Wed, Apr 7, 2010 at 2:55 PM, Hooiveld, Guido <guido.hooiveld@wur.nl>wrote: > Dear list, > I am trying to build an annotation package for the Mouse Gene 1.1 ST > Array Plate (GeneTitan peg array) using pdInfoBuilder. As input i use > the PGF, CLF, etc files downloaded from Affymetrix. However, the > following lines of code do not work; specifically I am puzzled by the > error message that a file is in the wrong "format". Can someone please > explain what this error means (i have never heard of 'ScalarCharacter'), > and how to solve it? > Thanks, > Guido > > http://www.affymetrix.com/browse/products.jsp?productId=131555&navMo de=3 > 4000&navAction=jump&aId=productsNav#1_3<http: www.affymetrix.com="" br="" owse="" products.jsp?productid="131555&amp;navMode=3%0A4000&amp;navAction=jump&amp;aId" =productsnav#1_3=""> > > > > library("pdInfoBuilder") > Loading required package: Biobase > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > 'openVignette()'. To cite Bioconductor, see > 'citation("Biobase")' and for packages 'citation(pkgname)'. > > Loading required package: RSQLite > Loading required package: DBI > Loading required package: affxparser > Loading required package: oligo > Loading required package: oligoClasses > Loading required package: preprocessCore > Welcome to oligo version 1.10.0 > > > > pgfFile = "MoGene-1_1-st-v1.r4.pgf"; > > clfFile = "MoGene-1_1-st-v1.r4.clf"; > > probeFile = "MoGene-1_1-st-v1.mm8.probe.tab"; > > transFile = "MoGene-1_1-st-v1.na30.1.mm9.transcript.csv"; > > pkg <- new("AffyGenePDInfoPkgSeed", > + version="0.0.1", > + author="Guido Hooiveld", email=guido.hooiveld@xxx, > + biocViews="AnnotationData", > + genomebuild="mm8", > + pgfFile=pgfFile, clfFile=clfFile, > + probeFile=probeFile, transFile=transFile); > Error in validObject(.Object) : > invalid class "AffyGenePDInfoPkgSeed" object: invalid object for slot > "transFile" > in class "AffyGenePDInfoPkgSeed": got class "character", > should be or extend class "ScalarCharacter" > > sessionInfo() > R version 2.10.1 (2009-12-14) > x86_64-unknown-linux-gnu > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > > other attached packages: > [1] pdInfoBuilder_1.10.1 oligo_1.10.0 preprocessCore_1.8.0 > [4] oligoClasses_1.8.0 affxparser_1.18.0 RSQLite_0.8-0 > [7] DBI_0.2-5 Biobase_2.6.1 > > loaded via a namespace (and not attached): > [1] affyio_1.14.0 Biostrings_2.14.10 IRanges_1.4.9 > splines_2.10.1 > [5] tools_2.10.1 > > > > > ------------------------------------------------ > Guido Hooiveld, PhD > Nutrition, Metabolism & Genomics Group > Division of Human Nutrition > Wageningen University > Biotechnion, Bomenweg 2 > NL-6703 HD Wageningen > the Netherlands > tel: (+)31 317 485788 > fax: (+)31 317 483342 > internet: http://nutrigene.4t.com <http: nutrigene.4t.com=""/> > email: guido.hooiveld@wur.nl > > > > [[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 > [[alternative HTML version deleted]]
ADD COMMENTlink written 9.5 years ago by Vincent J. Carey, Jr.6.3k
Thanks Vince, that did the trick. Working fine now. Guido ________________________________ From: Vincent Carey [mailto:stvjc@channing.harvard.edu] Sent: 07 April 2010 21:48 To: Hooiveld, Guido Cc: bioconductor@stat.math.ethz.ch Subject: Re: [BioC] pdInfoBuilder: invalid class object ("ScalarCharacter") This is not a message about a file format. It says that the input to the class definition for slot transFile is of the wrong class. Try transFile = new("ScalarCharacter", [your filename]) and see where you get. Note > getClass("AffyGenePDInfoPkgSeed") Class "AffyGenePDInfoPkgSeed" [package "pdInfoBuilder"] Slots: Name: pgfFile clfFile probeFile transFile Class: ScalarCharacter ScalarCharacter ScalarCharacter ScalarCharacter Name: coreMps fullMps extendedMps geneArray Class: ScalarCharacter ScalarCharacter ScalarCharacter logical Name: version license author email Class: character character character character Name: biocViews chipName manufacturer url Class: character character character character Name: genomebuild organism species Class: character character character Extends: Class "AffySTPDInfoPkgSeed", directly Class "AffymetrixPDInfoPkgSeed", by class "AffySTPDInfoPkgSeed", distance 2 Class "PDInfoPkgSeed", by class "AffySTPDInfoPkgSeed", distance 3 showing that some of the slots need to be instances of ScalarCharacter, others can be plain character. Furthermore > getClass("ScalarCharacter") Class "ScalarCharacter" [package "Biobase"] Slots: Name: .Data Class: character Extends: Class "ScalarObject", directly Class "character", from data part Class "vector", by class "character", distance 2 Class "data.frameRowLabels", by class "character", distance 2 Class "characterORMIAME", by class "character", distance 2 note furthermore > getValidity(getClass("ScalarObject")) function (object) { if (length(object) != 1L) paste(class(object), "must have length one") else TRUE } <environment: namespace:biobase=""> On Wed, Apr 7, 2010 at 2:55 PM, Hooiveld, Guido <guido.hooiveld@wur.nl> wrote: Dear list, I am trying to build an annotation package for the Mouse Gene 1.1 ST Array Plate (GeneTitan peg array) using pdInfoBuilder. As input i use the PGF, CLF, etc files downloaded from Affymetrix. However, the following lines of code do not work; specifically I am puzzled by the error message that a file is in the wrong "format". Can someone please explain what this error means (i have never heard of 'ScalarCharacter'), and how to solve it? Thanks, Guido http://www.affymetrix.com/browse/products.jsp?productId=131555&navMode =3 4000&navAction=jump&aId=productsNav#1_3 <http: www.affymetrix.com="" browse="" products.jsp?productid="131555&amp;navMod" e="3%0A4000&amp;navAction=jump&amp;aId=productsNav#1_3"> > library("pdInfoBuilder") Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. Loading required package: RSQLite Loading required package: DBI Loading required package: affxparser Loading required package: oligo Loading required package: oligoClasses Loading required package: preprocessCore Welcome to oligo version 1.10.0 > > pgfFile = "MoGene-1_1-st-v1.r4.pgf"; > clfFile = "MoGene-1_1-st-v1.r4.clf"; > probeFile = "MoGene-1_1-st-v1.mm8.probe.tab"; > transFile = "MoGene-1_1-st-v1.na30.1.mm9.transcript.csv"; > pkg <- new("AffyGenePDInfoPkgSeed", + version="0.0.1", + author="Guido Hooiveld", email=guido.hooiveld@xxx, + biocViews="AnnotationData", + genomebuild="mm8", + pgfFile=pgfFile, clfFile=clfFile, + probeFile=probeFile, transFile=transFile); Error in validObject(.Object) : invalid class "AffyGenePDInfoPkgSeed" object: invalid object for slot "transFile" in class "AffyGenePDInfoPkgSeed": got class "character", should be or extend class "ScalarCharacter" > sessionInfo() R version 2.10.1 (2009-12-14) x86_64-unknown-linux-gnu locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] pdInfoBuilder_1.10.1 oligo_1.10.0 preprocessCore_1.8.0 [4] oligoClasses_1.8.0 affxparser_1.18.0 RSQLite_0.8-0 [7] DBI_0.2-5 Biobase_2.6.1 loaded via a namespace (and not attached): [1] affyio_1.14.0 Biostrings_2.14.10 IRanges_1.4.9 splines_2.10.1 [5] tools_2.10.1 ------------------------------------------------ Guido Hooiveld, PhD Nutrition, Metabolism & Genomics Group Division of Human Nutrition Wageningen University Biotechnion, Bomenweg 2 NL-6703 HD Wageningen the Netherlands tel: (+)31 317 485788 fax: (+)31 317 483342 internet: http://nutrigene.4t.com <http: nutrigene.4t.com=""/> email: guido.hooiveld@wur.nl [[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 [[alternative HTML version deleted]]
ADD REPLYlink written 9.5 years ago by Guido Hooiveld2.5k
i assume you're aware that this package is available for download via biocLite()... the updated version, with na30, will be released with the next bioc. b On Wed, Apr 7, 2010 at 10:17 PM, Hooiveld, Guido <guido.hooiveld at="" wur.nl=""> wrote: > Thanks Vince, that did the trick. > Working fine now. > Guido > > > ________________________________ > > ? ? ? ?From: Vincent Carey [mailto:stvjc at channing.harvard.edu] > ? ? ? ?Sent: 07 April 2010 21:48 > ? ? ? ?To: Hooiveld, Guido > ? ? ? ?Cc: bioconductor at stat.math.ethz.ch > ? ? ? ?Subject: Re: [BioC] pdInfoBuilder: invalid class object > ("ScalarCharacter") > > > ? ? ? ?This is not a message about a file format. ?It says that the > input to the class definition for slot transFile is of the wrong class. > Try > > ? ? ? ?transFile = new("ScalarCharacter", [your filename]) > > ? ? ? ?and see where you get. ?Note > > ? ? ? ?> getClass("AffyGenePDInfoPkgSeed") > ? ? ? ?Class "AffyGenePDInfoPkgSeed" [package "pdInfoBuilder"] > > ? ? ? ?Slots: > > > ? ? ? ?Name: ? ? ? ? ?pgfFile ? ? ? ? clfFile ? ? ? probeFile > transFile > ? ? ? ?Class: ScalarCharacter ScalarCharacter ScalarCharacter > ScalarCharacter > > > ? ? ? ?Name: ? ? ? ? ?coreMps ? ? ? ? fullMps ? ? extendedMps > geneArray > ? ? ? ?Class: ScalarCharacter ScalarCharacter ScalarCharacter > logical > > > ? ? ? ?Name: ? ? ? ? ?version ? ? ? ? license ? ? ? ? ?author > email > ? ? ? ?Class: ? ? ? character ? ? ? character ? ? ? character > character > > > ? ? ? ?Name: ? ? ? ?biocViews ? ? ? ?chipName ? ?manufacturer > url > ? ? ? ?Class: ? ? ? character ? ? ? character ? ? ? character > character > > ? ? ? ?Name: ? ? ?genomebuild ? ? ? ?organism ? ? ? ? species > ? ? ? ?Class: ? ? ? character ? ? ? character ? ? ? character > > ? ? ? ?Extends: > ? ? ? ?Class "AffySTPDInfoPkgSeed", directly > ? ? ? ?Class "AffymetrixPDInfoPkgSeed", by class "AffySTPDInfoPkgSeed", > distance 2 > ? ? ? ?Class "PDInfoPkgSeed", by class "AffySTPDInfoPkgSeed", distance > 3 > > ? ? ? ?showing that some of the slots need to be instances of > ScalarCharacter, others can be plain character. ?Furthermore > > ? ? ? ?> getClass("ScalarCharacter") > ? ? ? ?Class "ScalarCharacter" [package "Biobase"] > > ? ? ? ?Slots: > > ? ? ? ?Name: ? ? ?.Data > ? ? ? ?Class: character > > ? ? ? ?Extends: > ? ? ? ?Class "ScalarObject", directly > ? ? ? ?Class "character", from data part > ? ? ? ?Class "vector", by class "character", distance 2 > ? ? ? ?Class "data.frameRowLabels", by class "character", distance 2 > ? ? ? ?Class "characterORMIAME", by class "character", distance 2 > > ? ? ? ?note furthermore > > ? ? ? ?> getValidity(getClass("ScalarObject")) > ? ? ? ?function (object) > ? ? ? ?{ > ? ? ? ? ? ?if (length(object) != 1L) > ? ? ? ? ? ? ? ?paste(class(object), "must have length one") > ? ? ? ? ? ?else TRUE > ? ? ? ?} > ? ? ? ?<environment: namespace:biobase=""> > > > > > > ? ? ? ?On Wed, Apr 7, 2010 at 2:55 PM, Hooiveld, Guido > <guido.hooiveld at="" wur.nl=""> wrote: > > > ? ? ? ? ? ? ? ?Dear list, > ? ? ? ? ? ? ? ?I am trying to build an annotation package for the Mouse > Gene 1.1 ST > ? ? ? ? ? ? ? ?Array Plate (GeneTitan peg array) using pdInfoBuilder. > As input i use > ? ? ? ? ? ? ? ?the PGF, CLF, etc files downloaded from Affymetrix. > However, the > ? ? ? ? ? ? ? ?following lines of code do not work; specifically I am > puzzled by the > ? ? ? ? ? ? ? ?error message that a file is in the wrong "format". Can > someone please > ? ? ? ? ? ? ? ?explain what this error means (i have never heard of > 'ScalarCharacter'), > ? ? ? ? ? ? ? ?and how to solve it? > ? ? ? ? ? ? ? ?Thanks, > ? ? ? ? ? ? ? ?Guido > > > http://www.affymetrix.com/browse/products.jsp?productId=131555&navMo de=3 > ? ? ? ? ? ? ? ?4000&navAction=jump&aId=productsNav#1_3 > <http: www.affymetrix.com="" browse="" products.jsp?productid="131555&amp;navM" ode=""> 3%0A4000&navAction=jump&aId=productsNav#1_3> > > > ? ? ? ? ? ? ? ?> library("pdInfoBuilder") > ? ? ? ? ? ? ? ?Loading required package: Biobase > > ? ? ? ? ? ? ? ?Welcome to Bioconductor > > ? ? ? ? ? ? ? ? Vignettes contain introductory material. To view, type > ? ? ? ? ? ? ? ? 'openVignette()'. To cite Bioconductor, see > ? ? ? ? ? ? ? ? 'citation("Biobase")' and for packages > 'citation(pkgname)'. > > ? ? ? ? ? ? ? ?Loading required package: RSQLite > ? ? ? ? ? ? ? ?Loading required package: DBI > ? ? ? ? ? ? ? ?Loading required package: affxparser > ? ? ? ? ? ? ? ?Loading required package: oligo > ? ? ? ? ? ? ? ?Loading required package: oligoClasses > ? ? ? ? ? ? ? ?Loading required package: preprocessCore > ? ? ? ? ? ? ? ?Welcome to oligo version 1.10.0 > ? ? ? ? ? ? ? ?> > ? ? ? ? ? ? ? ?> pgfFile = "MoGene-1_1-st-v1.r4.pgf"; > ? ? ? ? ? ? ? ?> clfFile = "MoGene-1_1-st-v1.r4.clf"; > ? ? ? ? ? ? ? ?> probeFile = "MoGene-1_1-st-v1.mm8.probe.tab"; > ? ? ? ? ? ? ? ?> transFile = > "MoGene-1_1-st-v1.na30.1.mm9.transcript.csv"; > ? ? ? ? ? ? ? ?> pkg <- new("AffyGenePDInfoPkgSeed", > ? ? ? ? ? ? ? ?+ ? ? ? ? ? version="0.0.1", > ? ? ? ? ? ? ? ?+ ? ? ? ? ? author="Guido Hooiveld", > email=guido.hooiveld at xxx, > ? ? ? ? ? ? ? ?+ ? ? ? ? ? biocViews="AnnotationData", > ? ? ? ? ? ? ? ?+ ? ? ? ? ? genomebuild="mm8", > ? ? ? ? ? ? ? ?+ ? ? ? ? ? pgfFile=pgfFile, clfFile=clfFile, > ? ? ? ? ? ? ? ?+ ? ? ? ? ? probeFile=probeFile, transFile=transFile); > ? ? ? ? ? ? ? ?Error in validObject(.Object) : > ? ? ? ? ? ? ? ? invalid class "AffyGenePDInfoPkgSeed" object: invalid > object for slot > ? ? ? ? ? ? ? ?"transFile" > ? ? ? ? ? ? ? ?in class "AffyGenePDInfoPkgSeed": got class "character", > ? ? ? ? ? ? ? ?should be or extend class "ScalarCharacter" > ? ? ? ? ? ? ? ?> sessionInfo() > ? ? ? ? ? ? ? ?R version 2.10.1 (2009-12-14) > ? ? ? ? ? ? ? ?x86_64-unknown-linux-gnu > > ? ? ? ? ? ? ? ?locale: > ? ? ? ? ? ? ? ? [1] LC_CTYPE=en_US.UTF-8 ? ? ? LC_NUMERIC=C > ? ? ? ? ? ? ? ? [3] LC_TIME=en_US.UTF-8 ? ? ? ?LC_COLLATE=en_US.UTF-8 > ? ? ? ? ? ? ? ? [5] LC_MONETARY=C ? ? ? ? ? ? ?LC_MESSAGES=en_US.UTF-8 > ? ? ? ? ? ? ? ? [7] LC_PAPER=en_US.UTF-8 ? ? ? LC_NAME=C > ? ? ? ? ? ? ? ? [9] LC_ADDRESS=C ? ? ? ? ? ? ? LC_TELEPHONE=C > ? ? ? ? ? ? ? ?[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > ? ? ? ? ? ? ? ?attached base packages: > ? ? ? ? ? ? ? ?[1] stats ? ? graphics ?grDevices utils ? ? datasets > methods ? base > > > ? ? ? ? ? ? ? ?other attached packages: > ? ? ? ? ? ? ? ?[1] pdInfoBuilder_1.10.1 oligo_1.10.0 > preprocessCore_1.8.0 > ? ? ? ? ? ? ? ?[4] oligoClasses_1.8.0 ? affxparser_1.18.0 > RSQLite_0.8-0 > ? ? ? ? ? ? ? ?[7] DBI_0.2-5 ? ? ? ? ? ?Biobase_2.6.1 > > ? ? ? ? ? ? ? ?loaded via a namespace (and not attached): > ? ? ? ? ? ? ? ?[1] affyio_1.14.0 ? ? ?Biostrings_2.14.10 IRanges_1.4.9 > ? ? ? ? ? ? ? ?splines_2.10.1 > ? ? ? ? ? ? ? ?[5] tools_2.10.1 > > > > > ? ? ? ? ? ? ? ?------------------------------------------------ > ? ? ? ? ? ? ? ?Guido Hooiveld, PhD > ? ? ? ? ? ? ? ?Nutrition, Metabolism & Genomics Group > ? ? ? ? ? ? ? ?Division of Human Nutrition > ? ? ? ? ? ? ? ?Wageningen University > ? ? ? ? ? ? ? ?Biotechnion, Bomenweg 2 > ? ? ? ? ? ? ? ?NL-6703 HD Wageningen > ? ? ? ? ? ? ? ?the Netherlands > ? ? ? ? ? ? ? ?tel: (+)31 317 485788 > ? ? ? ? ? ? ? ?fax: (+)31 317 483342 > ? ? ? ? ? ? ? ?internet: ? http://nutrigene.4t.com > <http: nutrigene.4t.com=""/> > ? ? ? ? ? ? ? ?email: ? ? ?guido.hooiveld at wur.nl > > > > ? ? ? ? ? ? ? ? ? ? ? [[alternative HTML version deleted]] > > ? ? ? ? ? ? ? ?_______________________________________________ > ? ? ? ? ? ? ? ?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 > > > > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > 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 >
ADD REPLYlink written 9.5 years ago by Benilton Carvalho4.3k
Hi Benilton, Thanks for your suggestion. However, I did check before both release and dev annotation packages, but I could not found a pd package for this specific array. I assume you refer to pd.mogene.1.0.st.v1, http://www.bioconductor.org/packages/devel/data/annotation/html/pd.mog ene.1.0.st.v1.html which is for the cardridge mouse Gene ST array (=version 1.0) [MoGene- 1_0-st-v1], whereas I do have data generated on the peg (plate, GeneTitan) version of this array (= mouse Gene ST array version 1.1) [MoGene-1_1-st-v1]. Guido > -----Original Message----- > From: Benilton Carvalho [mailto:beniltoncarvalho at gmail.com] > Sent: 07 April 2010 23:26 > To: Hooiveld, Guido > Cc: Vincent Carey; bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] pdInfoBuilder: invalid class object > ("ScalarCharacter") > > i assume you're aware that this package is available for > download via biocLite()... the updated version, with na30, > will be released with the next bioc. b > > On Wed, Apr 7, 2010 at 10:17 PM, Hooiveld, Guido > <guido.hooiveld at="" wur.nl=""> wrote: > > Thanks Vince, that did the trick. > > Working fine now. > > Guido > > > > > > ________________________________ > > > > ? ? ? ?From: Vincent Carey [mailto:stvjc at channing.harvard.edu] > > ? ? ? ?Sent: 07 April 2010 21:48 > > ? ? ? ?To: Hooiveld, Guido > > ? ? ? ?Cc: bioconductor at stat.math.ethz.ch > > ? ? ? ?Subject: Re: [BioC] pdInfoBuilder: invalid class object > > ("ScalarCharacter") > > > > > > ? ? ? ?This is not a message about a file format. ?It says that the > > input to the class definition for slot transFile is of the > wrong class. > > Try > > > > ? ? ? ?transFile = new("ScalarCharacter", [your filename]) > > > > ? ? ? ?and see where you get. ?Note > > > > ? ? ? ?> getClass("AffyGenePDInfoPkgSeed") > > ? ? ? ?Class "AffyGenePDInfoPkgSeed" [package "pdInfoBuilder"] > > > > ? ? ? ?Slots: > > > > > > ? ? ? ?Name: ? ? ? ? ?pgfFile ? ? ? ? clfFile ? ? ? probeFile > > transFile > > ? ? ? ?Class: ScalarCharacter ScalarCharacter ScalarCharacter > > ScalarCharacter > > > > > > ? ? ? ?Name: ? ? ? ? ?coreMps ? ? ? ? fullMps ? ? extendedMps > > geneArray > > ? ? ? ?Class: ScalarCharacter ScalarCharacter > ScalarCharacter logical > > > > > > ? ? ? ?Name: ? ? ? ? ?version ? ? ? ? license ? ? ? ? ?author email > > ? ? ? ?Class: ? ? ? character ? ? ? character ? ? ? character > > character > > > > > > ? ? ? ?Name: ? ? ? ?biocViews ? ? ? ?chipName ? ?manufacturer url > > ? ? ? ?Class: ? ? ? character ? ? ? character ? ? ? character > > character > > > > ? ? ? ?Name: ? ? ?genomebuild ? ? ? ?organism ? ? ? ? species > > ? ? ? ?Class: ? ? ? character ? ? ? character ? ? ? character > > > > ? ? ? ?Extends: > > ? ? ? ?Class "AffySTPDInfoPkgSeed", directly > > ? ? ? ?Class "AffymetrixPDInfoPkgSeed", by class > > "AffySTPDInfoPkgSeed", distance 2 > > ? ? ? ?Class "PDInfoPkgSeed", by class > "AffySTPDInfoPkgSeed", distance > > 3 > > > > ? ? ? ?showing that some of the slots need to be instances of > > ScalarCharacter, others can be plain character. ?Furthermore > > > > ? ? ? ?> getClass("ScalarCharacter") > > ? ? ? ?Class "ScalarCharacter" [package "Biobase"] > > > > ? ? ? ?Slots: > > > > ? ? ? ?Name: ? ? ?.Data > > ? ? ? ?Class: character > > > > ? ? ? ?Extends: > > ? ? ? ?Class "ScalarObject", directly > > ? ? ? ?Class "character", from data part > > ? ? ? ?Class "vector", by class "character", distance 2 > > ? ? ? ?Class "data.frameRowLabels", by class "character", distance 2 > > ? ? ? ?Class "characterORMIAME", by class "character", distance 2 > > > > ? ? ? ?note furthermore > > > > ? ? ? ?> getValidity(getClass("ScalarObject")) > > ? ? ? ?function (object) > > ? ? ? ?{ > > ? ? ? ? ? ?if (length(object) != 1L) > > ? ? ? ? ? ? ? ?paste(class(object), "must have length one") > > ? ? ? ? ? ?else TRUE > > ? ? ? ?} > > ? ? ? ?<environment: namespace:biobase=""> > > > > > > > > > > > > ? ? ? ?On Wed, Apr 7, 2010 at 2:55 PM, Hooiveld, Guido > > <guido.hooiveld at="" wur.nl=""> wrote: > > > > > > ? ? ? ? ? ? ? ?Dear list, > > ? ? ? ? ? ? ? ?I am trying to build an annotation package for the > > Mouse Gene 1.1 ST > > ? ? ? ? ? ? ? ?Array Plate (GeneTitan peg array) using > pdInfoBuilder. > > As input i use > > ? ? ? ? ? ? ? ?the PGF, CLF, etc files downloaded from Affymetrix. > > However, the > > ? ? ? ? ? ? ? ?following lines of code do not work; > specifically I am > > puzzled by the > > ? ? ? ? ? ? ? ?error message that a file is in the wrong > "format". Can > > someone please > > ? ? ? ? ? ? ? ?explain what this error means (i have never heard of > > 'ScalarCharacter'), > > ? ? ? ? ? ? ? ?and how to solve it? > > ? ? ? ? ? ? ? ?Thanks, > > ? ? ? ? ? ? ? ?Guido > > > > > > > http://www.affymetrix.com/browse/products.jsp?productId=131555&navMode > > =3 > > ? ? ? ? ? ? ? ?4000&navAction=jump&aId=productsNav#1_3 > > > <http: www.affymetrix.com="" browse="" products.jsp?productid="131555&amp;navMod"> > e= 3%0A4000&navAction=jump&aId=productsNav#1_3> > > > > > > ? ? ? ? ? ? ? ?> library("pdInfoBuilder") > > ? ? ? ? ? ? ? ?Loading required package: Biobase > > > > ? ? ? ? ? ? ? ?Welcome to Bioconductor > > > > ? ? ? ? ? ? ? ? Vignettes contain introductory material. To > view, type > > ? ? ? ? ? ? ? ? 'openVignette()'. To cite Bioconductor, see > > ? ? ? ? ? ? ? ? 'citation("Biobase")' and for packages > > 'citation(pkgname)'. > > > > ? ? ? ? ? ? ? ?Loading required package: RSQLite > > ? ? ? ? ? ? ? ?Loading required package: DBI > > ? ? ? ? ? ? ? ?Loading required package: affxparser > > ? ? ? ? ? ? ? ?Loading required package: oligo > > ? ? ? ? ? ? ? ?Loading required package: oligoClasses > > ? ? ? ? ? ? ? ?Loading required package: preprocessCore > > ? ? ? ? ? ? ? ?Welcome to oligo version 1.10.0 > > ? ? ? ? ? ? ? ?> > > ? ? ? ? ? ? ? ?> pgfFile = "MoGene-1_1-st-v1.r4.pgf"; > > ? ? ? ? ? ? ? ?> clfFile = "MoGene-1_1-st-v1.r4.clf"; > > ? ? ? ? ? ? ? ?> probeFile = "MoGene-1_1-st-v1.mm8.probe.tab"; > > ? ? ? ? ? ? ? ?> transFile = > > "MoGene-1_1-st-v1.na30.1.mm9.transcript.csv"; > > ? ? ? ? ? ? ? ?> pkg <- new("AffyGenePDInfoPkgSeed", > > ? ? ? ? ? ? ? ?+ ? ? ? ? ? version="0.0.1", > > ? ? ? ? ? ? ? ?+ ? ? ? ? ? author="Guido Hooiveld", > > email=guido.hooiveld at xxx, > > ? ? ? ? ? ? ? ?+ ? ? ? ? ? biocViews="AnnotationData", > > ? ? ? ? ? ? ? ?+ ? ? ? ? ? genomebuild="mm8", > > ? ? ? ? ? ? ? ?+ ? ? ? ? ? pgfFile=pgfFile, clfFile=clfFile, > > ? ? ? ? ? ? ? ?+ ? ? ? ? ? probeFile=probeFile, > transFile=transFile); > > ? ? ? ? ? ? ? ?Error in validObject(.Object) : > > ? ? ? ? ? ? ? ? invalid class "AffyGenePDInfoPkgSeed" > object: invalid > > object for slot > > ? ? ? ? ? ? ? ?"transFile" > > ? ? ? ? ? ? ? ?in class "AffyGenePDInfoPkgSeed": got class > > "character", > > ? ? ? ? ? ? ? ?should be or extend class "ScalarCharacter" > > ? ? ? ? ? ? ? ?> sessionInfo() > > ? ? ? ? ? ? ? ?R version 2.10.1 (2009-12-14) > > ? ? ? ? ? ? ? ?x86_64-unknown-linux-gnu > > > > ? ? ? ? ? ? ? ?locale: > > ? ? ? ? ? ? ? ? [1] LC_CTYPE=en_US.UTF-8 ? ? ? LC_NUMERIC=C > > ? ? ? ? ? ? ? ? [3] LC_TIME=en_US.UTF-8 ? ? ? ? > LC_COLLATE=en_US.UTF-8 > > ? ? ? ? ? ? ? ? [5] LC_MONETARY=C ? ? ? ? ? ? ? > LC_MESSAGES=en_US.UTF-8 > > ? ? ? ? ? ? ? ? [7] LC_PAPER=en_US.UTF-8 ? ? ? LC_NAME=C > > ? ? ? ? ? ? ? ? [9] LC_ADDRESS=C ? ? ? ? ? ? ? LC_TELEPHONE=C > > ? ? ? ? ? ? ? ?[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > ? ? ? ? ? ? ? ?attached base packages: > > ? ? ? ? ? ? ? ?[1] stats ? ? graphics ?grDevices utils ? ? datasets > > methods ? base > > > > > > ? ? ? ? ? ? ? ?other attached packages: > > ? ? ? ? ? ? ? ?[1] pdInfoBuilder_1.10.1 oligo_1.10.0 > > preprocessCore_1.8.0 > > ? ? ? ? ? ? ? ?[4] oligoClasses_1.8.0 ? affxparser_1.18.0 > > RSQLite_0.8-0 > > ? ? ? ? ? ? ? ?[7] DBI_0.2-5 ? ? ? ? ? ?Biobase_2.6.1 > > > > ? ? ? ? ? ? ? ?loaded via a namespace (and not attached): > > ? ? ? ? ? ? ? ?[1] affyio_1.14.0 ? ? ?Biostrings_2.14.10 > IRanges_1.4.9 > > ? ? ? ? ? ? ? ?splines_2.10.1 > > ? ? ? ? ? ? ? ?[5] tools_2.10.1 > > > > > > > > > > ? ? ? ? ? ? ? ?------------------------------------------------ > > ? ? ? ? ? ? ? ?Guido Hooiveld, PhD > > ? ? ? ? ? ? ? ?Nutrition, Metabolism & Genomics Group > > ? ? ? ? ? ? ? ?Division of Human Nutrition > > ? ? ? ? ? ? ? ?Wageningen University > > ? ? ? ? ? ? ? ?Biotechnion, Bomenweg 2 > > ? ? ? ? ? ? ? ?NL-6703 HD Wageningen > > ? ? ? ? ? ? ? ?the Netherlands > > ? ? ? ? ? ? ? ?tel: (+)31 317 485788 > > ? ? ? ? ? ? ? ?fax: (+)31 317 483342 > > ? ? ? ? ? ? ? ?internet: ? http://nutrigene.4t.com > > <http: nutrigene.4t.com=""/> > > ? ? ? ? ? ? ? ?email: ? ? ?guido.hooiveld at wur.nl > > > > > > > > ? ? ? ? ? ? ? ? ? ? ? [[alternative HTML version deleted]] > > > > ? ? ? ? ? ? ? ?_______________________________________________ > > ? ? ? ? ? ? ? ?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 > > > > > > > > > > ? ? ? ?[[alternative HTML version deleted]] > > > > _______________________________________________ > > 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 > > > >
ADD REPLYlink written 9.5 years ago by Guido Hooiveld2.5k
Aha! I conveniently skipped the 'Gene Titan' part, huh? I'll take a look at them, thanks, b On Thu, Apr 8, 2010 at 11:04 AM, Hooiveld, Guido <guido.hooiveld at="" wur.nl=""> wrote: > Hi Benilton, > > Thanks for your suggestion. However, I did check before both release and dev annotation packages, but I could not found a pd package for this specific array. > > I assume you refer to pd.mogene.1.0.st.v1, > http://www.bioconductor.org/packages/devel/data/annotation/html/pd.m ogene.1.0.st.v1.html > which is for the cardridge mouse Gene ST array (=version 1.0) [MoGene-1_0-st-v1], > whereas I do have data generated on the peg (plate, GeneTitan) version of this array (= mouse Gene ST array version 1.1) [MoGene- 1_1-st-v1]. > > Guido > > > >> -----Original Message----- >> From: Benilton Carvalho [mailto:beniltoncarvalho at gmail.com] >> Sent: 07 April 2010 23:26 >> To: Hooiveld, Guido >> Cc: Vincent Carey; bioconductor at stat.math.ethz.ch >> Subject: Re: [BioC] pdInfoBuilder: invalid class object >> ("ScalarCharacter") >> >> i assume you're aware that this package is available for >> download via biocLite()... the updated version, with na30, >> will be released with the next bioc. b >> >> On Wed, Apr 7, 2010 at 10:17 PM, Hooiveld, Guido >> <guido.hooiveld at="" wur.nl=""> wrote: >> > Thanks Vince, that did the trick. >> > Working fine now. >> > Guido >> > >> > >> > ________________________________ >> > >> > ? ? ? ?From: Vincent Carey [mailto:stvjc at channing.harvard.edu] >> > ? ? ? ?Sent: 07 April 2010 21:48 >> > ? ? ? ?To: Hooiveld, Guido >> > ? ? ? ?Cc: bioconductor at stat.math.ethz.ch >> > ? ? ? ?Subject: Re: [BioC] pdInfoBuilder: invalid class object >> > ("ScalarCharacter") >> > >> > >> > ? ? ? ?This is not a message about a file format. ?It says that the >> > input to the class definition for slot transFile is of the >> wrong class. >> > Try >> > >> > ? ? ? ?transFile = new("ScalarCharacter", [your filename]) >> > >> > ? ? ? ?and see where you get. ?Note >> > >> > ? ? ? ?> getClass("AffyGenePDInfoPkgSeed") >> > ? ? ? ?Class "AffyGenePDInfoPkgSeed" [package "pdInfoBuilder"] >> > >> > ? ? ? ?Slots: >> > >> > >> > ? ? ? ?Name: ? ? ? ? ?pgfFile ? ? ? ? clfFile ? ? ? probeFile >> > transFile >> > ? ? ? ?Class: ScalarCharacter ScalarCharacter ScalarCharacter >> > ScalarCharacter >> > >> > >> > ? ? ? ?Name: ? ? ? ? ?coreMps ? ? ? ? fullMps ? ? extendedMps >> > geneArray >> > ? ? ? ?Class: ScalarCharacter ScalarCharacter >> ScalarCharacter logical >> > >> > >> > ? ? ? ?Name: ? ? ? ? ?version ? ? ? ? license ? ? ? ? ?author email >> > ? ? ? ?Class: ? ? ? character ? ? ? character ? ? ? character >> > character >> > >> > >> > ? ? ? ?Name: ? ? ? ?biocViews ? ? ? ?chipName ? ?manufacturer url >> > ? ? ? ?Class: ? ? ? character ? ? ? character ? ? ? character >> > character >> > >> > ? ? ? ?Name: ? ? ?genomebuild ? ? ? ?organism ? ? ? ? species >> > ? ? ? ?Class: ? ? ? character ? ? ? character ? ? ? character >> > >> > ? ? ? ?Extends: >> > ? ? ? ?Class "AffySTPDInfoPkgSeed", directly >> > ? ? ? ?Class "AffymetrixPDInfoPkgSeed", by class >> > "AffySTPDInfoPkgSeed", distance 2 >> > ? ? ? ?Class "PDInfoPkgSeed", by class >> "AffySTPDInfoPkgSeed", distance >> > 3 >> > >> > ? ? ? ?showing that some of the slots need to be instances of >> > ScalarCharacter, others can be plain character. ?Furthermore >> > >> > ? ? ? ?> getClass("ScalarCharacter") >> > ? ? ? ?Class "ScalarCharacter" [package "Biobase"] >> > >> > ? ? ? ?Slots: >> > >> > ? ? ? ?Name: ? ? ?.Data >> > ? ? ? ?Class: character >> > >> > ? ? ? ?Extends: >> > ? ? ? ?Class "ScalarObject", directly >> > ? ? ? ?Class "character", from data part >> > ? ? ? ?Class "vector", by class "character", distance 2 >> > ? ? ? ?Class "data.frameRowLabels", by class "character", distance 2 >> > ? ? ? ?Class "characterORMIAME", by class "character", distance 2 >> > >> > ? ? ? ?note furthermore >> > >> > ? ? ? ?> getValidity(getClass("ScalarObject")) >> > ? ? ? ?function (object) >> > ? ? ? ?{ >> > ? ? ? ? ? ?if (length(object) != 1L) >> > ? ? ? ? ? ? ? ?paste(class(object), "must have length one") >> > ? ? ? ? ? ?else TRUE >> > ? ? ? ?} >> > ? ? ? ?<environment: namespace:biobase=""> >> > >> > >> > >> > >> > >> > ? ? ? ?On Wed, Apr 7, 2010 at 2:55 PM, Hooiveld, Guido >> > <guido.hooiveld at="" wur.nl=""> wrote: >> > >> > >> > ? ? ? ? ? ? ? ?Dear list, >> > ? ? ? ? ? ? ? ?I am trying to build an annotation package for the >> > Mouse Gene 1.1 ST >> > ? ? ? ? ? ? ? ?Array Plate (GeneTitan peg array) using >> pdInfoBuilder. >> > As input i use >> > ? ? ? ? ? ? ? ?the PGF, CLF, etc files downloaded from Affymetrix. >> > However, the >> > ? ? ? ? ? ? ? ?following lines of code do not work; >> specifically I am >> > puzzled by the >> > ? ? ? ? ? ? ? ?error message that a file is in the wrong >> "format". Can >> > someone please >> > ? ? ? ? ? ? ? ?explain what this error means (i have never heard of >> > 'ScalarCharacter'), >> > ? ? ? ? ? ? ? ?and how to solve it? >> > ? ? ? ? ? ? ? ?Thanks, >> > ? ? ? ? ? ? ? ?Guido >> > >> > >> > >> http://www.affymetrix.com/browse/products.jsp?productId=131555&navMode >> > =3 >> > ? ? ? ? ? ? ? ?4000&navAction=jump&aId=productsNav#1_3 >> > >> <http: www.affymetrix.com="" browse="" products.jsp?productid="131555&amp;navMod">> > e= 3%0A4000&navAction=jump&aId=productsNav#1_3> >> > >> > >> > ? ? ? ? ? ? ? ?> library("pdInfoBuilder") >> > ? ? ? ? ? ? ? ?Loading required package: Biobase >> > >> > ? ? ? ? ? ? ? ?Welcome to Bioconductor >> > >> > ? ? ? ? ? ? ? ? Vignettes contain introductory material. To >> view, type >> > ? ? ? ? ? ? ? ? 'openVignette()'. To cite Bioconductor, see >> > ? ? ? ? ? ? ? ? 'citation("Biobase")' and for packages >> > 'citation(pkgname)'. >> > >> > ? ? ? ? ? ? ? ?Loading required package: RSQLite >> > ? ? ? ? ? ? ? ?Loading required package: DBI >> > ? ? ? ? ? ? ? ?Loading required package: affxparser >> > ? ? ? ? ? ? ? ?Loading required package: oligo >> > ? ? ? ? ? ? ? ?Loading required package: oligoClasses >> > ? ? ? ? ? ? ? ?Loading required package: preprocessCore >> > ? ? ? ? ? ? ? ?Welcome to oligo version 1.10.0 >> > ? ? ? ? ? ? ? ?> >> > ? ? ? ? ? ? ? ?> pgfFile = "MoGene-1_1-st-v1.r4.pgf"; >> > ? ? ? ? ? ? ? ?> clfFile = "MoGene-1_1-st-v1.r4.clf"; >> > ? ? ? ? ? ? ? ?> probeFile = "MoGene-1_1-st-v1.mm8.probe.tab"; >> > ? ? ? ? ? ? ? ?> transFile = >> > "MoGene-1_1-st-v1.na30.1.mm9.transcript.csv"; >> > ? ? ? ? ? ? ? ?> pkg <- new("AffyGenePDInfoPkgSeed", >> > ? ? ? ? ? ? ? ?+ ? ? ? ? ? version="0.0.1", >> > ? ? ? ? ? ? ? ?+ ? ? ? ? ? author="Guido Hooiveld", >> > email=guido.hooiveld at xxx, >> > ? ? ? ? ? ? ? ?+ ? ? ? ? ? biocViews="AnnotationData", >> > ? ? ? ? ? ? ? ?+ ? ? ? ? ? genomebuild="mm8", >> > ? ? ? ? ? ? ? ?+ ? ? ? ? ? pgfFile=pgfFile, clfFile=clfFile, >> > ? ? ? ? ? ? ? ?+ ? ? ? ? ? probeFile=probeFile, >> transFile=transFile); >> > ? ? ? ? ? ? ? ?Error in validObject(.Object) : >> > ? ? ? ? ? ? ? ? invalid class "AffyGenePDInfoPkgSeed" >> object: invalid >> > object for slot >> > ? ? ? ? ? ? ? ?"transFile" >> > ? ? ? ? ? ? ? ?in class "AffyGenePDInfoPkgSeed": got class >> > "character", >> > ? ? ? ? ? ? ? ?should be or extend class "ScalarCharacter" >> > ? ? ? ? ? ? ? ?> sessionInfo() >> > ? ? ? ? ? ? ? ?R version 2.10.1 (2009-12-14) >> > ? ? ? ? ? ? ? ?x86_64-unknown-linux-gnu >> > >> > ? ? ? ? ? ? ? ?locale: >> > ? ? ? ? ? ? ? ? [1] LC_CTYPE=en_US.UTF-8 ? ? ? LC_NUMERIC=C >> > ? ? ? ? ? ? ? ? [3] LC_TIME=en_US.UTF-8 >> LC_COLLATE=en_US.UTF-8 >> > ? ? ? ? ? ? ? ? [5] LC_MONETARY=C >> LC_MESSAGES=en_US.UTF-8 >> > ? ? ? ? ? ? ? ? [7] LC_PAPER=en_US.UTF-8 ? ? ? LC_NAME=C >> > ? ? ? ? ? ? ? ? [9] LC_ADDRESS=C ? ? ? ? ? ? ? LC_TELEPHONE=C >> > ? ? ? ? ? ? ? ?[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> > ? ? ? ? ? ? ? ?attached base packages: >> > ? ? ? ? ? ? ? ?[1] stats ? ? graphics ?grDevices utils ? ? datasets >> > methods ? base >> > >> > >> > ? ? ? ? ? ? ? ?other attached packages: >> > ? ? ? ? ? ? ? ?[1] pdInfoBuilder_1.10.1 oligo_1.10.0 >> > preprocessCore_1.8.0 >> > ? ? ? ? ? ? ? ?[4] oligoClasses_1.8.0 ? affxparser_1.18.0 >> > RSQLite_0.8-0 >> > ? ? ? ? ? ? ? ?[7] DBI_0.2-5 ? ? ? ? ? ?Biobase_2.6.1 >> > >> > ? ? ? ? ? ? ? ?loaded via a namespace (and not attached): >> > ? ? ? ? ? ? ? ?[1] affyio_1.14.0 ? ? ?Biostrings_2.14.10 >> IRanges_1.4.9 >> > ? ? ? ? ? ? ? ?splines_2.10.1 >> > ? ? ? ? ? ? ? ?[5] tools_2.10.1 >> > >> > >> > >> > >> > ? ? ? ? ? ? ? ?------------------------------------------------ >> > ? ? ? ? ? ? ? ?Guido Hooiveld, PhD >> > ? ? ? ? ? ? ? ?Nutrition, Metabolism & Genomics Group >> > ? ? ? ? ? ? ? ?Division of Human Nutrition >> > ? ? ? ? ? ? ? ?Wageningen University >> > ? ? ? ? ? ? ? ?Biotechnion, Bomenweg 2 >> > ? ? ? ? ? ? ? ?NL-6703 HD Wageningen >> > ? ? ? ? ? ? ? ?the Netherlands >> > ? ? ? ? ? ? ? ?tel: (+)31 317 485788 >> > ? ? ? ? ? ? ? ?fax: (+)31 317 483342 >> > ? ? ? ? ? ? ? ?internet: ? http://nutrigene.4t.com >> > <http: nutrigene.4t.com=""/> >> > ? ? ? ? ? ? ? ?email: ? ? ?guido.hooiveld at wur.nl >> > >> > >> > >> > ? ? ? ? ? ? ? ? ? ? ? [[alternative HTML version deleted]] >> > >> > ? ? ? ? ? ? ? ?_______________________________________________ >> > ? ? ? ? ? ? ? ?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 >> > >> > >> > >> > >> > ? ? ? ?[[alternative HTML version deleted]] >> > >> > _______________________________________________ >> > 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 >> > >> >> > >
ADD REPLYlink written 9.5 years ago by Benilton Carvalho4.3k
ok... i have just created the packages... they should appear on the next bioc release. b On Thu, Apr 8, 2010 at 11:04 AM, Hooiveld, Guido <guido.hooiveld at="" wur.nl=""> wrote: > Hi Benilton, > > Thanks for your suggestion. However, I did check before both release and dev annotation packages, but I could not found a pd package for this specific array. > > I assume you refer to pd.mogene.1.0.st.v1, > http://www.bioconductor.org/packages/devel/data/annotation/html/pd.m ogene.1.0.st.v1.html > which is for the cardridge mouse Gene ST array (=version 1.0) [MoGene-1_0-st-v1], > whereas I do have data generated on the peg (plate, GeneTitan) version of this array (= mouse Gene ST array version 1.1) [MoGene- 1_1-st-v1]. > > Guido > > > >> -----Original Message----- >> From: Benilton Carvalho [mailto:beniltoncarvalho at gmail.com] >> Sent: 07 April 2010 23:26 >> To: Hooiveld, Guido >> Cc: Vincent Carey; bioconductor at stat.math.ethz.ch >> Subject: Re: [BioC] pdInfoBuilder: invalid class object >> ("ScalarCharacter") >> >> i assume you're aware that this package is available for >> download via biocLite()... the updated version, with na30, >> will be released with the next bioc. b >> >> On Wed, Apr 7, 2010 at 10:17 PM, Hooiveld, Guido >> <guido.hooiveld at="" wur.nl=""> wrote: >> > Thanks Vince, that did the trick. >> > Working fine now. >> > Guido >> > >> > >> > ________________________________ >> > >> > ? ? ? ?From: Vincent Carey [mailto:stvjc at channing.harvard.edu] >> > ? ? ? ?Sent: 07 April 2010 21:48 >> > ? ? ? ?To: Hooiveld, Guido >> > ? ? ? ?Cc: bioconductor at stat.math.ethz.ch >> > ? ? ? ?Subject: Re: [BioC] pdInfoBuilder: invalid class object >> > ("ScalarCharacter") >> > >> > >> > ? ? ? ?This is not a message about a file format. ?It says that the >> > input to the class definition for slot transFile is of the >> wrong class. >> > Try >> > >> > ? ? ? ?transFile = new("ScalarCharacter", [your filename]) >> > >> > ? ? ? ?and see where you get. ?Note >> > >> > ? ? ? ?> getClass("AffyGenePDInfoPkgSeed") >> > ? ? ? ?Class "AffyGenePDInfoPkgSeed" [package "pdInfoBuilder"] >> > >> > ? ? ? ?Slots: >> > >> > >> > ? ? ? ?Name: ? ? ? ? ?pgfFile ? ? ? ? clfFile ? ? ? probeFile >> > transFile >> > ? ? ? ?Class: ScalarCharacter ScalarCharacter ScalarCharacter >> > ScalarCharacter >> > >> > >> > ? ? ? ?Name: ? ? ? ? ?coreMps ? ? ? ? fullMps ? ? extendedMps >> > geneArray >> > ? ? ? ?Class: ScalarCharacter ScalarCharacter >> ScalarCharacter logical >> > >> > >> > ? ? ? ?Name: ? ? ? ? ?version ? ? ? ? license ? ? ? ? ?author email >> > ? ? ? ?Class: ? ? ? character ? ? ? character ? ? ? character >> > character >> > >> > >> > ? ? ? ?Name: ? ? ? ?biocViews ? ? ? ?chipName ? ?manufacturer url >> > ? ? ? ?Class: ? ? ? character ? ? ? character ? ? ? character >> > character >> > >> > ? ? ? ?Name: ? ? ?genomebuild ? ? ? ?organism ? ? ? ? species >> > ? ? ? ?Class: ? ? ? character ? ? ? character ? ? ? character >> > >> > ? ? ? ?Extends: >> > ? ? ? ?Class "AffySTPDInfoPkgSeed", directly >> > ? ? ? ?Class "AffymetrixPDInfoPkgSeed", by class >> > "AffySTPDInfoPkgSeed", distance 2 >> > ? ? ? ?Class "PDInfoPkgSeed", by class >> "AffySTPDInfoPkgSeed", distance >> > 3 >> > >> > ? ? ? ?showing that some of the slots need to be instances of >> > ScalarCharacter, others can be plain character. ?Furthermore >> > >> > ? ? ? ?> getClass("ScalarCharacter") >> > ? ? ? ?Class "ScalarCharacter" [package "Biobase"] >> > >> > ? ? ? ?Slots: >> > >> > ? ? ? ?Name: ? ? ?.Data >> > ? ? ? ?Class: character >> > >> > ? ? ? ?Extends: >> > ? ? ? ?Class "ScalarObject", directly >> > ? ? ? ?Class "character", from data part >> > ? ? ? ?Class "vector", by class "character", distance 2 >> > ? ? ? ?Class "data.frameRowLabels", by class "character", distance 2 >> > ? ? ? ?Class "characterORMIAME", by class "character", distance 2 >> > >> > ? ? ? ?note furthermore >> > >> > ? ? ? ?> getValidity(getClass("ScalarObject")) >> > ? ? ? ?function (object) >> > ? ? ? ?{ >> > ? ? ? ? ? ?if (length(object) != 1L) >> > ? ? ? ? ? ? ? ?paste(class(object), "must have length one") >> > ? ? ? ? ? ?else TRUE >> > ? ? ? ?} >> > ? ? ? ?<environment: namespace:biobase=""> >> > >> > >> > >> > >> > >> > ? ? ? ?On Wed, Apr 7, 2010 at 2:55 PM, Hooiveld, Guido >> > <guido.hooiveld at="" wur.nl=""> wrote: >> > >> > >> > ? ? ? ? ? ? ? ?Dear list, >> > ? ? ? ? ? ? ? ?I am trying to build an annotation package for the >> > Mouse Gene 1.1 ST >> > ? ? ? ? ? ? ? ?Array Plate (GeneTitan peg array) using >> pdInfoBuilder. >> > As input i use >> > ? ? ? ? ? ? ? ?the PGF, CLF, etc files downloaded from Affymetrix. >> > However, the >> > ? ? ? ? ? ? ? ?following lines of code do not work; >> specifically I am >> > puzzled by the >> > ? ? ? ? ? ? ? ?error message that a file is in the wrong >> "format". Can >> > someone please >> > ? ? ? ? ? ? ? ?explain what this error means (i have never heard of >> > 'ScalarCharacter'), >> > ? ? ? ? ? ? ? ?and how to solve it? >> > ? ? ? ? ? ? ? ?Thanks, >> > ? ? ? ? ? ? ? ?Guido >> > >> > >> > >> http://www.affymetrix.com/browse/products.jsp?productId=131555&navMode >> > =3 >> > ? ? ? ? ? ? ? ?4000&navAction=jump&aId=productsNav#1_3 >> > >> <http: www.affymetrix.com="" browse="" products.jsp?productid="131555&amp;navMod">> > e= 3%0A4000&navAction=jump&aId=productsNav#1_3> >> > >> > >> > ? ? ? ? ? ? ? ?> library("pdInfoBuilder") >> > ? ? ? ? ? ? ? ?Loading required package: Biobase >> > >> > ? ? ? ? ? ? ? ?Welcome to Bioconductor >> > >> > ? ? ? ? ? ? ? ? Vignettes contain introductory material. To >> view, type >> > ? ? ? ? ? ? ? ? 'openVignette()'. To cite Bioconductor, see >> > ? ? ? ? ? ? ? ? 'citation("Biobase")' and for packages >> > 'citation(pkgname)'. >> > >> > ? ? ? ? ? ? ? ?Loading required package: RSQLite >> > ? ? ? ? ? ? ? ?Loading required package: DBI >> > ? ? ? ? ? ? ? ?Loading required package: affxparser >> > ? ? ? ? ? ? ? ?Loading required package: oligo >> > ? ? ? ? ? ? ? ?Loading required package: oligoClasses >> > ? ? ? ? ? ? ? ?Loading required package: preprocessCore >> > ? ? ? ? ? ? ? ?Welcome to oligo version 1.10.0 >> > ? ? ? ? ? ? ? ?> >> > ? ? ? ? ? ? ? ?> pgfFile = "MoGene-1_1-st-v1.r4.pgf"; >> > ? ? ? ? ? ? ? ?> clfFile = "MoGene-1_1-st-v1.r4.clf"; >> > ? ? ? ? ? ? ? ?> probeFile = "MoGene-1_1-st-v1.mm8.probe.tab"; >> > ? ? ? ? ? ? ? ?> transFile = >> > "MoGene-1_1-st-v1.na30.1.mm9.transcript.csv"; >> > ? ? ? ? ? ? ? ?> pkg <- new("AffyGenePDInfoPkgSeed", >> > ? ? ? ? ? ? ? ?+ ? ? ? ? ? version="0.0.1", >> > ? ? ? ? ? ? ? ?+ ? ? ? ? ? author="Guido Hooiveld", >> > email=guido.hooiveld at xxx, >> > ? ? ? ? ? ? ? ?+ ? ? ? ? ? biocViews="AnnotationData", >> > ? ? ? ? ? ? ? ?+ ? ? ? ? ? genomebuild="mm8", >> > ? ? ? ? ? ? ? ?+ ? ? ? ? ? pgfFile=pgfFile, clfFile=clfFile, >> > ? ? ? ? ? ? ? ?+ ? ? ? ? ? probeFile=probeFile, >> transFile=transFile); >> > ? ? ? ? ? ? ? ?Error in validObject(.Object) : >> > ? ? ? ? ? ? ? ? invalid class "AffyGenePDInfoPkgSeed" >> object: invalid >> > object for slot >> > ? ? ? ? ? ? ? ?"transFile" >> > ? ? ? ? ? ? ? ?in class "AffyGenePDInfoPkgSeed": got class >> > "character", >> > ? ? ? ? ? ? ? ?should be or extend class "ScalarCharacter" >> > ? ? ? ? ? ? ? ?> sessionInfo() >> > ? ? ? ? ? ? ? ?R version 2.10.1 (2009-12-14) >> > ? ? ? ? ? ? ? ?x86_64-unknown-linux-gnu >> > >> > ? ? ? ? ? ? ? ?locale: >> > ? ? ? ? ? ? ? ? [1] LC_CTYPE=en_US.UTF-8 ? ? ? LC_NUMERIC=C >> > ? ? ? ? ? ? ? ? [3] LC_TIME=en_US.UTF-8 >> LC_COLLATE=en_US.UTF-8 >> > ? ? ? ? ? ? ? ? [5] LC_MONETARY=C >> LC_MESSAGES=en_US.UTF-8 >> > ? ? ? ? ? ? ? ? [7] LC_PAPER=en_US.UTF-8 ? ? ? LC_NAME=C >> > ? ? ? ? ? ? ? ? [9] LC_ADDRESS=C ? ? ? ? ? ? ? LC_TELEPHONE=C >> > ? ? ? ? ? ? ? ?[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> > ? ? ? ? ? ? ? ?attached base packages: >> > ? ? ? ? ? ? ? ?[1] stats ? ? graphics ?grDevices utils ? ? datasets >> > methods ? base >> > >> > >> > ? ? ? ? ? ? ? ?other attached packages: >> > ? ? ? ? ? ? ? ?[1] pdInfoBuilder_1.10.1 oligo_1.10.0 >> > preprocessCore_1.8.0 >> > ? ? ? ? ? ? ? ?[4] oligoClasses_1.8.0 ? affxparser_1.18.0 >> > RSQLite_0.8-0 >> > ? ? ? ? ? ? ? ?[7] DBI_0.2-5 ? ? ? ? ? ?Biobase_2.6.1 >> > >> > ? ? ? ? ? ? ? ?loaded via a namespace (and not attached): >> > ? ? ? ? ? ? ? ?[1] affyio_1.14.0 ? ? ?Biostrings_2.14.10 >> IRanges_1.4.9 >> > ? ? ? ? ? ? ? ?splines_2.10.1 >> > ? ? ? ? ? ? ? ?[5] tools_2.10.1 >> > >> > >> > >> > >> > ? ? ? ? ? ? ? ?------------------------------------------------ >> > ? ? ? ? ? ? ? ?Guido Hooiveld, PhD >> > ? ? ? ? ? ? ? ?Nutrition, Metabolism & Genomics Group >> > ? ? ? ? ? ? ? ?Division of Human Nutrition >> > ? ? ? ? ? ? ? ?Wageningen University >> > ? ? ? ? ? ? ? ?Biotechnion, Bomenweg 2 >> > ? ? ? ? ? ? ? ?NL-6703 HD Wageningen >> > ? ? ? ? ? ? ? ?the Netherlands >> > ? ? ? ? ? ? ? ?tel: (+)31 317 485788 >> > ? ? ? ? ? ? ? ?fax: (+)31 317 483342 >> > ? ? ? ? ? ? ? ?internet: ? http://nutrigene.4t.com >> > <http: nutrigene.4t.com=""/> >> > ? ? ? ? ? ? ? ?email: ? ? ?guido.hooiveld at wur.nl >> > >> > >> > >> > ? ? ? ? ? ? ? ? ? ? ? [[alternative HTML version deleted]] >> > >> > ? ? ? ? ? ? ? ?_______________________________________________ >> > ? ? ? ? ? ? ? ?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 >> > >> > >> > >> > >> > ? ? ? ?[[alternative HTML version deleted]] >> > >> > _______________________________________________ >> > 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 >> > >> >> > >
ADD REPLYlink written 9.5 years ago by Benilton Carvalho4.3k
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