amigo links: gene ontology annotation for probes
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@colin-a-smith-325
Last seen 7.4 years ago
Germany
Yvonne- It looks like they changed their URL format. Please look for a fix in the next couple days in either annaffy 1.6.2 (Release 1.9) or 1.7.3 (Devel 2.0). Cheers. -Colin On Feb 19, 2007, at 4:49 , Yvonne J.K. Edwards wrote: > Hi, > > I am using Bioconductor to annotate some probes as described in the > chapter "Interactive Outputs". CA Smith, W Huber and R. Gentleman, in > the book "Bioinformatics and Computational Biology Solutions using > R and > Bioconductor". I created the HTML Table with annotation links and > I noticed that the Gene Ontology link to the Amigo homepage as > opposed to the GO term in the Amigo site. Judging how interactive the > other parts of the table are I am suspecting this is not what is > intended. > > A typical link would look like this > http://www.godatabase.org/cgi-bin/amigo/go.cgi?open_0=GO:0005554 > > but the browser displays the home page of amigo. > > > This is sample code > ------------------- > library("mgu74av2") > library("XML") > library("KEGG") > library("GO") > library("annotate") > library("annaffy") > probeId <- c("103753_at") > probeId > anncols <- aaf.handler()[c(1:13)] > anncols > annTable <- aafTableAnn(probeId,"mgu74av2", anncols) > saveHTML(annTable, "annotation.html", title = "Example Table with > Data") > > This is version of packages > --------------------------- > sessionInfo() > R version 2.4.0 (2006-10-03) > i686-pc-linux-gnu > locale: > LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB > .UTF-8;LC_ > MONETARY=en_GB.UTF-8;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_N > AME=C;LC_A > DDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C > attached base packages: > [1] "methods" "stats" "graphics" "grDevices" "utils" > "datasets" > [7] "base" > > other attached packages: > annaffy annotate Biobase GO KEGG XML mgu74av2 > "1.6.0" "1.12.0" "1.12.2" "1.14.0" "1.14.0" "1.4-1" "1.14.0" > > > Any suggestions about what I could do to remedy this ?? > > Thank you for your considerations, > Best wishes > Yvonne
Annotation GO Biobase annotate annaffy Annotation GO Biobase annotate annaffy • 695 views
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@yvonne-jk-edwards-2052
Last seen 8.1 years ago
Hi, I am using Bioconductor to annotate some probes as described in the chapter "Interactive Outputs". CA Smith, W Huber and R. Gentleman, in the book "Bioinformatics and Computational Biology Solutions using R and Bioconductor". I created the HTML Table with annotation links and I noticed that the Gene Ontology link to the Amigo homepage as opposed to the GO term in the Amigo site. Judging how interactive the other parts of the table are I am suspecting this is not what is intended. A typical link would look like this http://www.godatabase.org/cgi-bin/amigo/go.cgi?open_0=GO:0005554 but the browser displays the home page of amigo. This is sample code ------------------- library("mgu74av2") library("XML") library("KEGG") library("GO") library("annotate") library("annaffy") probeId <- c("103753_at") probeId anncols <- aaf.handler()[c(1:13)] anncols annTable <- aafTableAnn(probeId,"mgu74av2", anncols) saveHTML(annTable, "annotation.html", title = "Example Table with Data") This is version of packages --------------------------- sessionInfo() R version 2.4.0 (2006-10-03) i686-pc-linux-gnu locale: LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB .UTF-8;LC_ MONETARY=en_GB.UTF-8;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_N AME=C;LC_A DDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] "methods" "stats" "graphics" "grDevices" "utils" "datasets" [7] "base" other attached packages: annaffy annotate Biobase GO KEGG XML mgu74av2 "1.6.0" "1.12.0" "1.12.2" "1.14.0" "1.14.0" "1.4-1" "1.14.0" Any suggestions about what I could do to remedy this ?? Thank you for your considerations, Best wishes Yvonne -- ---------------------------------------------------------------------- Yvonne JK Edwards, PhD Senior Research Fellow Bioinformatics Unit Department of Computer Science University College London Gower Street, London, WC1E 6BT
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