Question: AnnBuilder and Kegg
0
gravatar for John Zhang
13.0 years ago by
John Zhang2.9k
John Zhang2.9k 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
ADD COMMENTlink modified 13.0 years ago by David Lapointe170 • written 13.0 years ago by John Zhang2.9k
Answer: AnnBuilder and Kegg
0
gravatar for John Zhang
13.0 years ago by
John Zhang2.9k
John Zhang2.9k wrote:
>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="ft 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.yeastgeno me.org/pub /yeast/sequence_similarity/domains/",KEGGGENOME="ftp://ftp.genome.ad.j p/pub/kegg /tarfiles/genome",PFAM="ftp://ftp.sanger.ac.uk/pub/databases/Pfam/curr ent_releas 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
ADD COMMENTlink written 13.0 years ago by John Zhang2.9k
Answer: AnnBuilder and Kegg
0
gravatar for John Zhang
13.0 years ago by
John Zhang2.9k
John Zhang2.9k wrote:
>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.yeastgen ome.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/cur rent_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
ADD COMMENTlink written 13.0 years ago by John Zhang2.9k
Answer: AnnBuilder and Kegg
0
gravatar for David Lapointe
13.0 years ago by
David Lapointe170 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@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@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.yeastgen om 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/cur re 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]] _______________________________________________ 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 COMMENTlink written 13.0 years ago by David Lapointe170
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/DA TA", > IPI="ftp > : > >//ftp.ebi.ac.uk/pub/databases/IPI/current/",YEAST="ftp://ftp.yeastg enom > e.org/pu > b > >/yeast/sequence_similarity/domains/",KEGGGENOME="ftp://ftp.genome.a d.jp > /pub/keg > g > >/tarfiles/genome",PFAM="ftp://ftp.sanger.ac.uk/pub/databases/Pfam/c urre > 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]] > > _______________________________________________ > 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 13.0 years ago by Paola Pedotti60
Answer: AnnBuilder and Kegg
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13.0 years ago by
Paola Pedotti60 wrote:
Dear John, thank you for the suggestions. However, I downloaded the newest version of AnnBuilder and still I had the same problem in kegg connection. ********************************************************************** ******************************************** 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="ftp ://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://ft p.yeastgenome.org/pub /yeast/sequence_similarity/domains/",KEGGGENOME= "ftp://ftp.genome.ad.jp/pub/kegg /tarfiles/genome",PFAM="ftp://ftp.san ger.ac.uk/pub/databases/Pfam/current_releas 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 >
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ADD COMMENTlink written 13.0 years ago by Paola Pedotti60
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/DAT A",IPI="ftp > > : > >>//ftp.ebi.ac.uk/pub/databases/IPI/current/",YEAST="ftp://ftp.yeastge nome.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/cu rrent_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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
ADD REPLYlink written 13.0 years ago by James W. MacDonald51k
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