[BioC] AnnBuilder and Kegg
James W. MacDonald
jmacdon at med.umich.edu
Wed Nov 22 17:24:31 CET 2006
You have mis-spelled Mus musculus each time.
Best,
Jim
Pedotti, P. (HKG) wrote:
> 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/pathways",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.yeastgenome.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/current_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
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>>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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--
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623
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