GO terms: Annotation for HumanMethylation450

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Marc Carlson ★ 7.2k

@marc-carlson-2264

Last seen 7.8 years ago

United States

Hi Fabrice, Suppose you are using Tims package. library("IlluminaHumanMethylation450k.db") That would give you access to this object: IlluminaHumanMethylation450kGO Which would allow you to get the GO IDs for all your probes etc. So then I think your question is: how could you get the GO terms and the pathways? Well how about doing this? library(GO.db) ids = c( "GO:0008150", "GO:0001869") ## just for example.. result = select(GO.db, keys =ids, cols=c("DEFINITION","TERM")) That value in result could then be merged (using the merge method) to your previous results (the ones that have the GOIDs) Marc On 03/29/2013 08:49 AM, Fabrice Tourre wrote: > Dear list, > > In the annotation file of Infinium HumanMethylation450 BeadChip, > http://support.illumina.com/documents/MyIllumina/b78d361a-def5-4adb- ab38-e8990625f053/HumanMethylation450_15017482_v.1.2.csv > > for each probe set, they do not have annotation for GO terms, pathways. > > As they have done in the annotation file: HG- U133_Plus_2.na32.annot.csv. > > Is there some bioconductor package to annotated the Infinium > HumanMethylation450 probes? Given a probe, feed back the GO terms and > pathways. > > Thank you very much in advance. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

Annotation Pathways GO probe Annotation Pathways GO probe • 1.1k views

ADD COMMENT • link updated 11.1 years ago by Jinyan Huang ▴ 110 • written 11.1 years ago by Marc Carlson ★ 7.2k

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Jinyan Huang ▴ 110

@jinyan-huang-5828

Last seen 9.7 years ago

Marc Carlson, Thank you. When I try your code, I have this problem. > library(GO.db) > ids = c( "GO:0008150", "GO:0001869") ## just for example.. > result = select(GO.db, keys =ids, cols=c("DEFINITION","TERM")) Error in eval(expr, envir, enclos) : object 'GODEFINITION' not found On Tue, Apr 2, 2013 at 5:03 PM, Marc Carlson <mcarlson at="" fhcrc.org=""> wrote: > Hi Fabrice, > > Suppose you are using Tims package. > > library("IlluminaHumanMethylation450k.db") > > That would give you access to this object: IlluminaHumanMethylation450kGO > > Which would allow you to get the GO IDs for all your probes etc. > > So then I think your question is: how could you get the GO terms and the > pathways? > > Well how about doing this? > > library(GO.db) > ids = c( "GO:0008150", "GO:0001869") ## just for example.. > result = select(GO.db, keys =ids, cols=c("DEFINITION","TERM")) > > That value in result could then be merged (using the merge method) to your > previous results (the ones that have the GOIDs) > > > Marc > > > > On 03/29/2013 08:49 AM, Fabrice Tourre wrote: >> >> Dear list, >> >> In the annotation file of Infinium HumanMethylation450 BeadChip, >> >> http://support.illumina.com/documents/MyIllumina/b78d361a-def5 -4adb-ab38-e8990625f053/HumanMethylation450_15017482_v.1.2.csv >> >> for each probe set, they do not have annotation for GO terms, pathways. >> >> As they have done in the annotation file: HG- U133_Plus_2.na32.annot.csv. >> >> Is there some bioconductor package to annotated the Infinium >> HumanMethylation450 probes? Given a probe, feed back the GO terms and >> pathways. >> >> Thank you very much in advance. >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- Best wishes, Jinyan HUANG

ADD COMMENT • link 11.1 years ago Jinyan Huang ▴ 110

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Hi Jinyan, I can't reproduce this problem in release or devel. So can you please follow the posting guidelines here: http://www.bioconductor.org/help/mailing-list/posting-guide/ And give me the output of your sessionInfo()? Thanks, Marc On 04/02/2013 02:09 PM, Jinyan Huang wrote: > result = select(GO.db, keys =ids, cols=c("DEFINITION","TERM"))

ADD REPLY • link 11.1 years ago Marc Carlson ★ 7.2k

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> library(GO.db) Loading required package: AnnotationDbi Loading required package: BiocGenerics Attaching package: ?BiocGenerics? The following object(s) are masked from ?package:stats?: xtabs The following object(s) are masked from ?package:base?: anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, lapply, Map, mapply, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int, rownames, sapply, setdiff, table, tapply, union, unique Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: DBI > ids = c( "GO:0008150", "GO:0001869") > result = select(GO.db, keys =ids, cols=c("DEFINITION","TERM")) Error in eval(expr, envir, enclos) : object 'GODEFINITION' not found > sessionInfo() R version 2.15.1 (2012-06-22) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] GO.db_2.7.1 RSQLite_0.11.2 DBI_0.2-5 [4] AnnotationDbi_1.18.4 Biobase_2.16.0 BiocGenerics_0.2.0 loaded via a namespace (and not attached): [1] IRanges_1.14.4 stats4_2.15.1 On Tue, Apr 2, 2013 at 6:28 PM, Marc Carlson <mcarlson at="" fhcrc.org=""> wrote: > Hi Jinyan, > > I can't reproduce this problem in release or devel. > > > So can you please follow the posting guidelines here: > > http://www.bioconductor.org/help/mailing-list/posting-guide/ > > And give me the output of your sessionInfo()? > > > Thanks, > > > Marc > > > > On 04/02/2013 02:09 PM, Jinyan Huang wrote: >> >> result = select(GO.db, keys =ids, cols=c("DEFINITION","TERM")) > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- Best wishes, Jinyan HUANG

ADD REPLY • link 11.1 years ago Jinyan Huang ▴ 110

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Wow. That is some old software you have there. You should really update pronto. At the very least, you probably need a newer version of R, AnnotationDbi, and GO.db. Whenever you see strange things happening, you should probably start by updating to the latest version of your software. Bioconductor has a very active development community, and so a year is actually a very long time to go without updates. Here is my sessionInfo() (this is my older version for R from the the older release last fall). And I note that even what I list here could be a bit more up to date than it presently is. R version 2.15.2 Patched (2012-11-04 r61084) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] GO.db_2.8.0 RSQLite_0.11.2 DBI_0.2-5 [4] AnnotationDbi_1.20.6 Biobase_2.18.0 BiocGenerics_0.4.0 [7] BiocInstaller_1.8.3 loaded via a namespace (and not attached): [1] IRanges_1.16.4 parallel_2.15.2 stats4_2.15.2 tools_2.15.2 And later this week, there should be another release with even newer software... Marc On 04/02/2013 03:32 PM, Jinyan Huang wrote: >> library(GO.db) > Loading required package: AnnotationDbi > Loading required package: BiocGenerics > > Attaching package: ?BiocGenerics? > > The following object(s) are masked from ?package:stats?: > > xtabs > > The following object(s) are masked from ?package:base?: > > anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, > get, intersect, lapply, Map, mapply, mget, order, paste, pmax, > pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int, > rownames, sapply, setdiff, table, tapply, union, unique > > Loading required package: Biobase > Welcome to Bioconductor > > Vignettes contain introductory material; view with > 'browseVignettes()'. To cite Bioconductor, see > 'citation("Biobase")', and for packages 'citation("pkgname")'. > > Loading required package: DBI > >> ids = c( "GO:0008150", "GO:0001869") >> result = select(GO.db, keys =ids, cols=c("DEFINITION","TERM")) > Error in eval(expr, envir, enclos) : object 'GODEFINITION' not found >> sessionInfo() > R version 2.15.1 (2012-06-22) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] GO.db_2.7.1 RSQLite_0.11.2 DBI_0.2-5 > [4] AnnotationDbi_1.18.4 Biobase_2.16.0 BiocGenerics_0.2.0 > > loaded via a namespace (and not attached): > [1] IRanges_1.14.4 stats4_2.15.1 > > On Tue, Apr 2, 2013 at 6:28 PM, Marc Carlson <mcarlson at="" fhcrc.org=""> wrote: >> Hi Jinyan, >> >> I can't reproduce this problem in release or devel. >> >> >> So can you please follow the posting guidelines here: >> >> http://www.bioconductor.org/help/mailing-list/posting-guide/ >> >> And give me the output of your sessionInfo()? >> >> >> Thanks, >> >> >> Marc >> >> >> >> On 04/02/2013 02:09 PM, Jinyan Huang wrote: >>> result = select(GO.db, keys =ids, cols=c("DEFINITION","TERM")) >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > >

ADD REPLY • link 11.1 years ago Marc Carlson ★ 7.2k

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