Question: AnnBuilder problem with custom List of genes
0
gravatar for claudio.is@libero.it
12.1 years ago by
claudio.is@libero.it210 wrote:
Dear BioC, I am trying to build up an annotation package for an old chips for which there is no annotation in BioC. I'am looking for AnnBuilder. First I create a file GEM.txt, with two columns, the first corresponds to probe location on the array (univocal numbers); the second corresponding to gene accession numbers. then I applied the following script. library(AnnBuilder) myBaseType <- "gb" mySrcUrls <- getSrcUrl("all", "Mus musculus") myDir <- "GEM_annotation" ABPkgBuilder(baseName = "GEM.txt", srcUrls = mySrcUrls, baseMapType =myBaseType, pkgName = "GEM",pkgPath = myDir, organism = "Mus musculus", version = "1.0.0",author = list(authors = "joe", maintainer ="joe.joe at gmail.com"), fromWeb = TRUE) after the creation of the package there is a little error in the DESCRIPTION file that is easly solved. The problem appears after the installation and the load of the package: actually no annotation is done. I get get following results. > GEM() Quality control information for GEM Date built: Created: Thu Aug 16 14:22:57 2007 Number of probes: 8734 Probe number missmatch: None Probe missmatch: None Mappings found for probe based rda files: GEMACCNUM found 8734 of 8734 GEMCHRLOC found 0 of 8734 GEMENTREZID found 0 of 8734 GEMENZYME found 0 of 8734 GEMPATH found 0 of 8734 Mappings found for non-probe based rda files: GEMCHRLENGTHS found 21 GEMORGANISM found 1 GEMPFAM found 0 GEMPROSITE found 0 Any suggestion?? -- Claudio Isella
ADD COMMENTlink modified 12.1 years ago • written 12.1 years ago by claudio.is@libero.it210
Answer: AnnBuilder problem with custom List of genes
0
gravatar for John Zhang
12.1 years ago by
John Zhang2.9k
John Zhang2.9k wrote:
> > >I am trying to build up an annotation package for an old chips for which there is no annotation in BioC. I'am looking for AnnBuilder. First I create a file GEM.txt, with two columns, the first corresponds to probe location on the array (univocal numbers); the second corresponding to gene accession numbers. You need to provide more information (e. g. your R and BioC version numbers (try sessionInfo()) and a few lines of your baseFile - GEM.txt). > >then I applied the following script. > >library(AnnBuilder) > >myBaseType <- "gb" > >mySrcUrls <- getSrcUrl("all", "Mus musculus") > >myDir <- "GEM_annotation" > >ABPkgBuilder(baseName = "GEM.txt", srcUrls = mySrcUrls, baseMapType =myBaseType, pkgName = "GEM",pkgPath = myDir, organism = "Mus musculus", version = "1.0.0",author = list(authors = "joe", maintainer ="joe.joe at gmail.com"), fromWeb = TRUE) > > >after the creation of the package there is a little error in the DESCRIPTION file that is easly solved. The problem appears after the installation and the load of the package: actually no annotation is done. I get get following results. > >> GEM() > >Quality control information for GEM >Date built: Created: Thu Aug 16 14:22:57 2007 > >Number of probes: 8734 >Probe number missmatch: None >Probe missmatch: None >Mappings found for probe based rda files: > GEMACCNUM found 8734 of 8734 > GEMCHRLOC found 0 of 8734 > GEMENTREZID found 0 of 8734 > GEMENZYME found 0 of 8734 > GEMPATH found 0 of 8734 >Mappings found for non-probe based rda files: > GEMCHRLENGTHS found 21 > GEMORGANISM found 1 > GEMPFAM found 0 > GEMPROSITE found 0 > >Any suggestion?? > >-- >Claudio Isella > >_______________________________________________ >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 Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084
ADD COMMENTlink written 12.1 years ago by John Zhang2.9k
Answer: AnnBuilder problem with custom List of genes
0
gravatar for claudio.is@libero.it
12.1 years ago by
claudio.is@libero.it210 wrote:
here it is. thanks R version 2.5.1 (2007-06-27) 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=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US. UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8 ;LC_IDENTIFICATION=C attached base packages: [1] "tools" "stats" "graphics" "grDevices" "utils" "datasets" [7] "methods" "base" other attached packages: AnnBuilder annotate XML Biobase GEM "1.14.0" "1.14.1" "1.9-0" "1.14.1" "1.0.0" ---------- Initial Header ----------- >From : "John Zhang" jzhang at jimmy.harvard.edu To : bioconductor at stat.math.ethz.ch, claudio.is at libero.it Cc : Date : Thu, 16 Aug 2007 13:52:41 -0400 (EDT) Subject : Re: [BioC] AnnBuilder problem with custom List of genes > > > > > > >I am trying to build up an annotation package for an old chips for which there > is no annotation in BioC. I'am looking for AnnBuilder. First I create a file > GEM.txt, with two columns, the first corresponds to probe location on the array > (univocal numbers); the second corresponding to gene accession numbers. > > > You need to provide more information (e. g. your R and BioC version numbers (try > sessionInfo()) and a few lines of your baseFile - GEM.txt). > > > > >then I applied the following script. > > > >library(AnnBuilder) > > > >myBaseType <- "gb" > > > >mySrcUrls <- getSrcUrl("all", "Mus musculus") > > > >myDir <- "GEM_annotation" > > > >ABPkgBuilder(baseName = "GEM.txt", srcUrls = mySrcUrls, baseMapType > =myBaseType, pkgName = "GEM",pkgPath = myDir, organism = "Mus musculus", version > = "1.0.0",author = list(authors = "joe", maintainer ="joe.joe at gmail.com"), > fromWeb = TRUE) > > > > > >after the creation of the package there is a little error in the DESCRIPTION > file that is easly solved. The problem appears after the installation and the > load of the package: actually no annotation is done. I get get following > results. > > > >> GEM() > > > >Quality control information for GEM > >Date built: Created: Thu Aug 16 14:22:57 2007 > > > >Number of probes: 8734 > >Probe number missmatch: None > >Probe missmatch: None > >Mappings found for probe based rda files: > > GEMACCNUM found 8734 of 8734 > > GEMCHRLOC found 0 of 8734 > > GEMENTREZID found 0 of 8734 > > GEMENZYME found 0 of 8734 > > GEMPATH found 0 of 8734 > >Mappings found for non-probe based rda files: > > GEMCHRLENGTHS found 21 > > GEMORGANISM found 1 > > GEMPFAM found 0 > > GEMPROSITE found 0 > > > >Any suggestion?? > > > >-- > >Claudio Isella > > > >_______________________________________________ > >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 > > Jianhua Zhang > Department of Medical Oncology > Dana-Farber Cancer Institute > 44 Binney Street > Boston, MA 02115-6084 >
ADD COMMENTlink written 12.1 years ago by claudio.is@libero.it210
claudio.is at libero.it wrote: > here it is. thanks > > > R version 2.5.1 (2007-06-27) > 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=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_U S.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF -8;LC_IDENTIFICATION=C > > attached base packages: > [1] "tools" "stats" "graphics" "grDevices" "utils" "datasets" > [7] "methods" "base" > > other attached packages: > AnnBuilder annotate XML Biobase GEM > "1.14.0" "1.14.1" "1.9-0" "1.14.1" "1.0.0" > > > > ---------- Initial Header ----------- > > >From : "John Zhang" jzhang at jimmy.harvard.edu > To : bioconductor at stat.math.ethz.ch, claudio.is at libero.it > Cc : > Date : Thu, 16 Aug 2007 13:52:41 -0400 (EDT) > Subject : Re: [BioC] AnnBuilder problem with custom List of genes > > > > > > > > >>> I am trying to build up an annotation package for an old chips for which there >>> >> is no annotation in BioC. I'am looking for AnnBuilder. First I create a file >> GEM.txt, with two columns, the first corresponds to probe location on the array >> (univocal numbers); the second corresponding to gene accession numbers. >> >> >> You need to provide more information (e. g. your R and BioC version numbers (try >> sessionInfo()) and a few lines of your baseFile - GEM.txt). >> >> >>> then I applied the following script. >>> >>> library(AnnBuilder) >>> >>> myBaseType <- "gb" >>> >>> mySrcUrls <- getSrcUrl("all", "Mus musculus") >>> >>> myDir <- "GEM_annotation" >>> >>> ABPkgBuilder(baseName = "GEM.txt", srcUrls = mySrcUrls, baseMapType >>> >> =myBaseType, pkgName = "GEM",pkgPath = myDir, organism = "Mus musculus", version >> = "1.0.0",author = list(authors = "joe", maintainer ="joe.joe at gmail.com"), >> fromWeb = TRUE) >> >>> after the creation of the package there is a little error in the DESCRIPTION >>> >> file that is easly solved. The problem appears after the installation and the >> load of the package: actually no annotation is done. I get get following >> results. >> >>>> GEM() >>>> >>> Quality control information for GEM >>> Date built: Created: Thu Aug 16 14:22:57 2007 >>> >>> Number of probes: 8734 >>> Probe number missmatch: None >>> Probe missmatch: None >>> Mappings found for probe based rda files: >>> GEMACCNUM found 8734 of 8734 >>> GEMCHRLOC found 0 of 8734 >>> GEMENTREZID found 0 of 8734 >>> GEMENZYME found 0 of 8734 >>> GEMPATH found 0 of 8734 >>> Mappings found for non-probe based rda files: >>> GEMCHRLENGTHS found 21 >>> GEMORGANISM found 1 >>> GEMPFAM found 0 >>> GEMPROSITE found 0 >>> >>> Any suggestion?? >>> >>> -- >>> Claudio Isella >>> >>> _______________________________________________ >>> 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 >> >> Jianhua Zhang >> Department of Medical Oncology >> Dana-Farber Cancer Institute >> 44 Binney Street >> Boston, MA 02115-6084 >> >> > > _______________________________________________ > 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 > > Hi Claudio, I cannot seem to reproduce this problem. Would you mind giving us a few of your accession numbers too? Marc
ADD REPLYlink written 12.1 years ago by Marc Carlson7.2k
Answer: AnnBuilder problem with custom List of genes
0
gravatar for claudio.is@libero.it
12.1 years ago by
claudio.is@libero.it210 wrote:
this is the top of my input file "A25" "AA415819" "A26" "AA474746" "A27" "AA473306" "A28" "AA545607" "A29" "AA413090" "A30" "AA386616" "A31" "AA437482" "A32" "AA412921" "A33" "AI508650" "A34" "AA386794" is it correct? ---------- Initial Header ----------- >From : "Marc Carlson" mcarlson at fhcrc.org To : "claudio.is at libero.it" claudio.is at libero.it Cc : "jzhang" jzhang at jimmy.harvard.edu,"bioconductor" bioconductor at stat.math.ethz.ch Date : Thu, 16 Aug 2007 15:02:03 -0700 Subject : Re: [BioC] AnnBuilder problem with custom List of genes > claudio.is at libero.it wrote: > > here it is. thanks > > > > > > R version 2.5.1 (2007-06-27) > > x86_64-unknown-linux-gnu > > > > locale: > > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=e n_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en _US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.U TF-8;LC_IDENTIFICATION=C > > > > attached base packages: > > [1] "tools" "stats" "graphics" "grDevices" "utils" "datasets" > > [7] "methods" "base" > > > > other attached packages: > > AnnBuilder annotate XML Biobase GEM > > "1.14.0" "1.14.1" "1.9-0" "1.14.1" "1.0.0" > > > > > > > > ---------- Initial Header ----------- > > > > >From : "John Zhang" jzhang at jimmy.harvard.edu > > To : bioconductor at stat.math.ethz.ch, claudio.is at libero.it > > Cc : > > Date : Thu, 16 Aug 2007 13:52:41 -0400 (EDT) > > Subject : Re: [BioC] AnnBuilder problem with custom List of genes > > > > > > > > > > > > > > > > > >>> I am trying to build up an annotation package for an old chips for which there > >>> > >> is no annotation in BioC. I'am looking for AnnBuilder. First I create a file > >> GEM.txt, with two columns, the first corresponds to probe location on the array > >> (univocal numbers); the second corresponding to gene accession numbers. > >> > >> > >> You need to provide more information (e. g. your R and BioC version numbers (try > >> sessionInfo()) and a few lines of your baseFile - GEM.txt). > >> > >> > >>> then I applied the following script. > >>> > >>> library(AnnBuilder) > >>> > >>> myBaseType <- "gb" > >>> > >>> mySrcUrls <- getSrcUrl("all", "Mus musculus") > >>> > >>> myDir <- "GEM_annotation" > >>> > >>> ABPkgBuilder(baseName = "GEM.txt", srcUrls = mySrcUrls, baseMapType > >>> > >> =myBaseType, pkgName = "GEM",pkgPath = myDir, organism = "Mus musculus", version > >> = "1.0.0",author = list(authors = "joe", maintainer ="joe.joe at gmail.com"), > >> fromWeb = TRUE) > >> > >>> after the creation of the package there is a little error in the DESCRIPTION > >>> > >> file that is easly solved. The problem appears after the installation and the > >> load of the package: actually no annotation is done. I get get following > >> results. > >> > >>>> GEM() > >>>> > >>> Quality control information for GEM > >>> Date built: Created: Thu Aug 16 14:22:57 2007 > >>> > >>> Number of probes: 8734 > >>> Probe number missmatch: None > >>> Probe missmatch: None > >>> Mappings found for probe based rda files: > >>> GEMACCNUM found 8734 of 8734 > >>> GEMCHRLOC found 0 of 8734 > >>> GEMENTREZID found 0 of 8734 > >>> GEMENZYME found 0 of 8734 > >>> GEMPATH found 0 of 8734 > >>> Mappings found for non-probe based rda files: > >>> GEMCHRLENGTHS found 21 > >>> GEMORGANISM found 1 > >>> GEMPFAM found 0 > >>> GEMPROSITE found 0 > >>> > >>> Any suggestion?? > >>> > >>> -- > >>> Claudio Isella > >>> > >>> _______________________________________________ > >>> 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 > >> > >> Jianhua Zhang > >> Department of Medical Oncology > >> Dana-Farber Cancer Institute > >> 44 Binney Street > >> Boston, MA 02115-6084 > >> > >> > > > > _______________________________________________ > > 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 > > > > > Hi Claudio, > > I cannot seem to reproduce this problem. Would you mind giving us a few > of your accession numbers too? > > Marc >
ADD COMMENTlink written 12.1 years ago by claudio.is@libero.it210
claudio.is at libero.it wrote: > this is the top of my input file > > "A25" "AA415819" > "A26" "AA474746" > "A27" "AA473306" > "A28" "AA545607" > "A29" "AA413090" > "A30" "AA386616" > "A31" "AA437482" > "A32" "AA412921" > "A33" "AI508650" > "A34" "AA386794" > > is it correct? > > > ---------- Initial Header ----------- > > >From : "Marc Carlson" mcarlson at fhcrc.org > To : "claudio.is at libero.it" claudio.is at libero.it > Cc : "jzhang" jzhang at jimmy.harvard.edu,"bioconductor" bioconductor at stat.math.ethz.ch > Date : Thu, 16 Aug 2007 15:02:03 -0700 > Subject : Re: [BioC] AnnBuilder problem with custom List of genes > > > > Nope. You don't want the quotes, and this file needs to be strictly tab delimited (not spaces). When I run your IDs as you have them listed here, I reproduce your bug and get empty fields. But when I clean them up so that they match the reccomendations in the AnnBuilder vignette (ie. just plain strings separated by tabs), then they work just fine. You might also find the following helpful: http://www.bioconductor.org/repository/devel/vignette/AnnBuilder.pdf Good luck with your project, Marc
ADD REPLYlink written 12.1 years ago by Marc Carlson7.2k
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