[BioC] AnnBuilder and Kegg
Paola Pedotti
p.pedotti at lumc.nl
Thu Nov 23 12:05:55 CET 2006
Thank you very much.
it is working now.
p
On Wed, 2006-11-22 at 11:25 -0500, Lapointe, David wrote:
> I believe it is Mus Musculus (see
> http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=10088 )
>
> David
>
> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch
> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Pedotti, P.
> (HKG)
> Sent: Wednesday, November 22, 2006 11:02 AM
> To: John Zhang; jzhang at jimmy.harvard.edu
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] AnnBuilder and Kegg
>
> Dear John,
> thank you again for the suggestions,
> but unfortunately I've got the same output with
>
>
> organism="Mus Musclusus"
>
> organism="Mus Musclus"
>
> organism="Mus musclus"
>
> organism="Mouse"
>
>
>
>
> -----Original Message-----
> From: John Zhang [mailto:jzhang at jimmy.harvard.edu]
> Sent: Wed 11/22/2006 3:29 PM
> To: jzhang at jimmy.harvard.edu; Pedotti, P. (HKG)
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] AnnBuilder and Kegg
>
>
> >After the program finishes I eventually have an annotation package for
> >my data but it does not contain any kegg data.
>
> Look at your code. The organism name is wrong (Mus Musclusus rather than
> Mus
> musclus).
>
> >
> >When I install my package (outside R, under linux)
> >I have this:
> >
> >***********************************************************************
> ********
> ***
> >R CMD INSTALL lgtc201106
> >* Installing *source* package 'lgtc201106' ...
> >** R
> >** data
> >** moving datasets to lazyload DB
> >** help
> > >>> Building/Updating help pages for package 'lgtc201106'
> > Formats: text html latex example
> > lgtc201106 text html latex
> > lgtc201106ACCNUM text html latex example
> > lgtc201106CHR text html latex example
> > lgtc201106ENZYME text html latex example
> > lgtc201106GENENAME text html latex example
> > lgtc201106GO text html latex example
> > lgtc201106GO2ALLPROBES text html latex example
> > lgtc201106GO2PROBE text html latex example
> > lgtc201106LOCUSID text html latex example
> > lgtc201106MAP text html latex example
> > lgtc201106OMIM text html latex example
> > lgtc201106ORGANISM text html latex example
> > lgtc201106PATH text html latex example
> > lgtc201106PMID text html latex example
> > lgtc201106PMID2PROBE text html latex example
> > lgtc201106QC text html latex
> > lgtc201106QCDATA text html latex
> > lgtc201106REFSEQ text html latex example
> > lgtc201106SUMFUNC text html latex example
> > lgtc201106SYMBOL text html latex example
> > lgtc201106UNIGENE text html latex example
> >** buil0ding package indices ...
> >* DONE (lgtc201106)
> >***********************************************************************
> ********
> **********
> >
> >and when I call the library in R
> >***********************************************************************
> ********
> **********
> >library(lgtc201106)
> >lgtc201106()
> >
> >
> >Quality control information for lgtc201106
> >Date built: Created: Wed Nov 22 13:12:38 2006
> >
> >Number of probes: 23233
> >Probe number missmatch: None
> >Probe missmatch: None
> >Mappings found for probe based rda files:
> > lgtc201106ACCNUM found 22512 of 23233
> > lgtc201106CHR found 18757 of 23233
> > lgtc201106ENZYME found 0 of 23233
> > lgtc201106GENENAME found 18674 of 23233
> > lgtc201106GO found 0 of 23233
> > lgtc201106GO found 0 of 23233
> > lgtc201106LOCUSID found 18977 of 23233
> > lgtc201106MAP found 15808 of 23233
> > lgtc201106OMIM found 433 of 23233
> > lgtc201106PATH found 0 of 23233
> > lgtc201106PMID found 18967 of 23233
> > lgtc201106REFSEQ found 14098 of 23233
> > lgtc201106SUMFUNC found 0 of 23233
> > lgtc201106SYMBOL found 18977 of 23233
> > lgtc201106UNIGENE found 18149 of 23233
> >Mappings found for non-probe based rda files:
> > lgtc201106GO2ALLPROBES found 6994
> > lgtc201106GO2PROBE found 5360
> > lgtc201106ORGANISM found 1
> > lgtc201106PMID2PROBE found 92300
> >
> >kegg <- as.list(lgtc201106PATH2PROBE)
> >Error: object "lgtc201106PATH2PROBE" not found
> >Error in as.list(lgtc201106PATH2PROBE) : unable to find the argument
> 'x' in
> selecting a method for function 'as.list'
> >
> >
> >***********************************************************************
> ********
> ****************************************
> >
> >thanks
> >
> >P
> >
> >
> >
> >-----Original Message-----
> >From: John Zhang [mailto:jzhang at jimmy.harvard.edu]
> >Sent: Wed 11/22/2006 2:25 PM
> >To: jzhang at jimmy.harvard.edu; Pedotti, P. (HKG)
> >Cc: bioconductor at stat.math.ethz.ch
> >Subject: Re: [BioC] AnnBuilder and Kegg
> >
> >
> >>thank you for the suggestions.
> >>However, I downloaded the newest version of AnnBuilder
> >>and still I had the same problem in kegg connection.
> >
> >Have you looked at the built package to see if you get any pathway
> annotation.
> >The warning messages like:
> >
> >Failed to get data from URL:
> >ftp://ftp.genome.ad.jp/pub/kegg/pathways//00010.gene
> >
> >just tell you that there are name miss-match in KEGG's data files but
> the data
> >package should still build.
> >
> >I will try to write more informative warning messages when I get the
> chance.
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >>
> >>**********************************************************************
> ********
> *
> >***********************************
> >>
> >>sessionInfo()
> >>Version 2.3.1 (2006-06-01)
> >>i386-pc-linux-gnu
> >>
> >>attached base packages:
> >>[1] "tools" "methods" "stats" "graphics" "grDevices"
> "utils"
> >>[7] "datasets" "base"
> >>
> >>other attached packages:
> >> GO AnnBuilder RSQLite DBI annotate XML
> >>Biobase
> >> "1.12.0" "1.12.0" "0.4-1" "0.1-10" "1.10.0" "0.99-7"
> >>"1.10.0"
> >>
> >>mySrcUrls <- c(GO=
> >>"http://www.godatabase.org/dev/database/archive/latest/go_2
> >>00605-termdb.rdf-xml.gz",KEGG="ftp://ftp.genome.ad.jp/pub/kegg/pathway
> s",YG="f
> t
> >p
> >://genome-ftp.stanford.edu/pub/yeast/data_download/",HG="ftp://ftp.ncbi
> .nih.gov
> /
> >pub/HomoloGene/old/hmlg.ftp",EG="ftp://ftp.ncbi.nlm.nih.gov/gene/DATA",
> IPI="ftp
> :
> >//ftp.ebi.ac.uk/pub/databases/IPI/current/",YEAST="ftp://ftp.yeastgenom
> e.org/pu
> b
> >/yeast/sequence_similarity/domains/",KEGGGENOME="ftp://ftp.genome.ad.jp
> /pub/keg
> g
> >/tarfiles/genome",PFAM="ftp://ftp.sanger.ac.uk/pub/databases/Pfam/curre
> nt_relea
> s
> >e/Pfam-A.full.gz")
> >>ppbase<- file.path(.path.package("AnnBuilder"), "data",
> >>"lgtc.ids.1.txt")
> >>myBaseType="gb"
> >>ABPkgBuilder(baseName=ppbase,
> >>+ srcUrls = mySrcUrls,
> >>+ baseMapType = myBaseType,
> >>+ pkgName = "lgtc.221106",
> >>+ pkgPath = '.',
> >>+ organism ="mouse",
> >>+ version ="1.1.0",
> >>+ author = list(author = "Paola Pedotti",
> >>+ maintener ="Paola Pedotti
> <p.pedotti at lumc.nl>")
> >>+ )
> >>
> >>Failed to get data from URL:
> >>ftp://ftp.genome.ad.jp/pub/kegg/pathways//00010.gene
> >>Failed to get data from URL:
> >>ftp://ftp.genome.ad.jp/pub/kegg/pathways//00020.gene
> >>Failed to get data from URL:
> >>ftp://ftp.genome.ad.jp/pub/kegg/pathways//00030.gene
> >>Failed to get data from URL:
> >>ftp://ftp.genome.ad.jp/pub/kegg/pathways//00031.gene
> >>Failed to get data from URL:
> >>ftp://ftp.genome.ad.jp/pub/kegg/pathways//00040.gene
> >>Failed to get data from URL:
> >>ftp://ftp.genome.ad.jp/pub/kegg/pathways//00051.gene
> >>Failed to get data from URL:
> >>ftp://ftp.genome.ad.jp/pub/kegg/pathways//00052.gene
> >>Failed to get data from URL:
> >>ftp://ftp.genome.ad.jp/pub/kegg/pathways//00053.gene
> >>Failed to get data from URL:
> >>ftp://ftp.genome.ad.jp/pub/kegg/pathways//00061.gene
> >>Failed to get data from URL:
> >>ftp://ftp.genome.ad.jp/pub/kegg/pathways//00062.gene
> >>Failed to get data from URL:
> >>ftp://ftp.genome.ad.jp/pub/kegg/pathways//00071.gene
> >>Failed to get data from URL:
> >>ftp://ftp.genome.ad.jp/pub/kegg/pathways//00072.gene
> >>Failed to get data from URL:
> >>ftp://ftp.genome.ad.jp/pub/kegg/pathways//00100.gene
> >>......................
> >>
> >>
> >>**********************************************************************
> ********
> *
> >****************************
> >>
> >>
> >>Do you have other suggestions?
> >>
> >>thanks
> >>
> >>Paola
> >>
> >>
> >>On Tue, 2006-11-21 at 12:13 -0500, John Zhang wrote:
> >>> >
> >>> >Hi everybody,
> >>> >I am trying to annotate my dataset (home spotted array, two colors,
> >>> >mice) using AnnBuilder.
> >>> >Every time I run the program the connection with the kegg
> >>> >website is not working, so I am able to build the annotation
> >>> >package but not for the kegg pathways. Does anybody know how to
> >>> >fix this problem or did anybody find a way to by pass it (like
> >>> >downloading a list of accession numbers and corresponding
> pathways)?
> >>> >here my script:
> >>>
> >>> I guess the best thing for you to do is to update your R and BioC
> packages.
> >The
> >>> released version of AnnBuilder is 1.12.0 while you have 1.10.0 on
> your
> >machine.
> >>>
> >>>
> >>>
> >>> >
> >>>
> >>**********************************************************************
> ********
> *
> >>> **********************
> >>> >
> >>> >library(AnnBuilder)
> >>> >#Loading required package: Biobase
> >>> >#Loading required package: tools
> >>> >#Welcome to Bioconductor
> >>> ># Vignettes contain introductory material. To view,
> >>> ># simply type: openVignette()
> >>> ># For details on reading vignettes, see
> >>> ># the openVignette help page.
> >>> >#Loading required package: annotate
> >>> >
> >>> >library(GO)
> >>> >
> >>> >sessionInfo()
> >>> >
> >>> >#Version 2.3.1 (2006-06-01)
> >>> >#i386-pc-linux-gnu
> >>> >#
> >>> >#attached base packages:
> >>> >#[1] "splines" "tools" "methods" "stats" "graphics"
> >>> >#"grDevices"
> >>> >#[7] "utils" "datasets" "base"
> >>> >#
> >>> >#other attached packages:
> >>> >#
> >>> ># globaltest vsn limma
> multtest
> >>> ># "4.2.0" "1.10.0" "2.7.3"
> "1.10.2"
> >>> ># survival affydata affy
> affyio
> >>> ># "2.20" "1.8.0" "1.10.0"
> "1.0.0"
> >>> ># KEGG GO AnnBuilder RSQLite
> >>> ># "1.12.0" "1.12.0" "1.10.0"
> "0.4-1"
> >>> ># DBI annotate XML
> Biobase
> >>> ># "0.1-10" "1.10.0" "0.99-7"
> "1.10.0"
> >>> >
> >>> >
> >>> >mySrcUrls <- getSrcUrl("all", organism="Mus Musclusus")
> >>> >
> >>> >base<- file.path(.path.package("AnnBuilder"), "data",
> "lgtc.ids.1.txt")
> >>> >
> >>> >myBaseType<- "gbNRef"
> >>> >ABPkgBuilder(baseName=base,
> >>> > srcUrls = mySrcUrls,
> >>> > baseMapType = myBaseType,
> >>> > pkgName = "lgtc201106",
> >>> > pkgPath = ".",
> >>> > organism ="Mus Musclusus",
> >>> > version ="1.1.0",
> >>> > author = list(author = "Paola Pedotti",
> >>> > maintener ="Paola Pedotti
> <p.pedotti at lumc.nl>")
> >>> > )
> >>> >
> >>> >
> >>> >#Failed to get data from URL:
> >>> >ftp://ftp.genome.ad.jp/pub/kegg/pathways//07214.gene
> >>> >#Failed to get data from URL:
> >>> >ftp://ftp.genome.ad.jp/pub/kegg/pathways//07215.gene
> >>> >#Failed to get data from URL:
> >>> >ftp://ftp.genome.ad.jp/pub/kegg/pathways//07216.gene
> >>> >#Failed to get data from URL:
> >>> >ftp://ftp.genome.ad.jp/pub/kegg/pathways//07217.gene
> >>> >#Failed to get data from URL:
> >>> >ftp://ftp.genome.ad.jp/pub/kegg/pathways//07218.gene
> >>> >#[1] "0 2 2"
> >>> >#Warning message:
> >>> >#cannot open file
> >>>
> >'/usr/local/lib/R/site-library/AnnBuilder/templates/PKGNAMEGO.1.Rd',
> >>> >reason 'No such file or directory'
> >>> >#The following data sets have been added to the database and will
> be
> >>> >removed:
> >>> ># [1] "./lgtc161106/data/lgtc161106ACCNUM.rda"
> >>> ># [2] "./lgtc161106/data/lgtc161106CHR.rda"
> >>> ># [3] "./lgtc161106/data/lgtc161106ENZYME.rda"
> >>> ># [4] "./lgtc161106/data/lgtc161106GENENAME.rda"
> >>> ># [5] "./lgtc161106/data/lgtc161106GO.1.rda"
> >>> ># [6] "./lgtc161106/data/lgtc161106GO2ALLPROBES.rda"
> >>> ># [7] "./lgtc161106/data/lgtc161106GO2PROBE.rda"
> >>> ># [8] "./lgtc161106/data/lgtc161106GO.rda"
> >>> ># [9] "./lgtc161106/data/lgtc161106LOCUSID.rda"
> >>> >#[10] "./lgtc161106/data/lgtc161106MAPCOUNTS.rda"
> >>> >#[11] "./lgtc161106/data/lgtc161106MAP.rda"
> >>> >#[12] "./lgtc161106/data/lgtc161106OMIM.rda"
> >>> >#[13] "./lgtc161106/data/lgtc161106ORGANISM.rda"
> >>> >#[14] "./lgtc161106/data/lgtc161106PATH.rda"
> >>> >#[15] "./lgtc161106/data/lgtc161106PMID2PROBE.rda"
> >>> >#[16] "./lgtc161106/data/lgtc161106PMID.rda"
> >>> >#[17] "./lgtc161106/data/lgtc161106QCDATA.rda"
> >>> >#[18] "./lgtc161106/data/lgtc161106QC.rda"
> >>> >#[19] "./lgtc161106/data/lgtc161106REFSEQ.rda"
> >>> >#[20] "./lgtc161106/data/lgtc161106SUMFUNC.rda"
> >>> >#[21] "./lgtc161106/data/lgtc161106SYMBOL.rda"
> >>> >#[22] "./lgtc161106/data/lgtc161106UNIGENE.rda"
> >>> >#Warning message:
> >>> >#Can't
> >>> >copy
> /usr/local/lib/R/site-library/AnnBuilder/templates/PKGNAMEGO.1.Rd
> >>> >in: copyTemplates(repList, pattern, pkgName, pkgPath)
> >>> >
> >>>
> >>**********************************************************************
> ********
> *
> >>> **********************
> >>> >
> >>> >
> >>> >thank you in advance
> >>> >
> >>> >Paola
> >>> >
> >>> >
> >>> >
> >>> >_______________________________________
> >>> >Center for Human and Clinical Genetics
> >>> >Leiden University Medical Center
> >>> >Postzone: S-04-P, Postbus 9600
> >>> >2300 RC Leiden, The Netherlands
> >>> >Telephone: +31 71 526 9440
> >>> >Fax: +31 71 526 8285
> >>> >
> >>> >_______________________________________________
> >>> >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
> >
> >Jianhua Zhang
> >Department of Medical Oncology
> >Dana-Farber Cancer Institute
> >44 Binney Street
> >Boston, MA 02115-6084
> >
> >
> >
> > [[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
>
> Jianhua Zhang
> Department of Medical Oncology
> Dana-Farber Cancer Institute
> 44 Binney Street
> Boston, MA 02115-6084
>
>
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
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