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Hi, I used GOstats to perform enrichment test on a set of genes (20). There are 7 GO terms with pvalue less than cuttoff and therefore shown in the result table. How can I get the information that which gene in the input gene set belong to which GO term of these enriched GO terms? Thanks for any comments. best,...

-----Original Message----- From: Robert Gentleman [mailto:rgentlem@fhcrc.org] Sent: Wed 10/12/2008 18:47 To: Legaie, Roxane Subject: Re: Kegg.db with GOstats Hi Roxanne, Can you redirect your question to the mailing list. And, you can find the answer in the mailing list archives... best wishes Robert Legaie, Roxane wrote: > Dear Robert Gentleman, > I am currently working on Streptomyces coelicolor microarray data. > > I have so...

I am running R 2.0.0, GOstats 1.1.1 and GO 1.7.0, and when I use the function GOHyperG, I have the following error: w1<-as.list(hgu95av2LOCUSID) w2<-unique(unlist(w1)) set.seed(123) myLL<-sample(w2,100) xx <- GOHyperG(myLL) Error in mget(x, env = GOTERM, ifnotfound = NA) : recursive default argument reference...

...(Windows based version) and downloaded Bioconductor available for this version via the graphical interface facility provided by R. Then installed GO 1.8.2 using the zip package, all goes well... I just tried to take a look at the output of GOLOCUSID2GO like Yu-An Dong have done it after loading GOstats (1.4.0) package : // GOLOCUSID2GO[["4121"]] //Then, after a while, R hangs up, windows tells my the program Rgui.exe is to be close by windows. So here, I don't think impatience is the explanaition of this problem :-( If anyone could give my a few hints, it would be great. Thanks...

...y Drnevich wrote: >Hi Jim & all, > >I'm having trouble getting affycoretools to work. I apparently had >downloaded & installed affycoretools before, but had never used it. When I >tried to load it today, I got an error message saying I was missing a >dependent package, GOstats. So I used biocLite() to download & install >GOstats & it's dependencies. Then when I tried to load affycoretools, I >crashed my Rgui. I restarted the Rgui a few times in different ways, and >each time I tried to load affycoretools, it crashed the Rgui. So then I >went and d...

Hello, R experts, I tried to retrieve all biological process GO terms at level 3 starting "biological process" as level 1 using the code as bellows: 1 library(GO) 2 library(GOstats) 3 level2<-getGOChildren("GO:0008150")$"GO:0008150"$Children 4 for ( i in 1:length(level2)) { 5 level3 <- getGOChildren(level2[i])$level2[i]$Children 6 for ( j in 1:length(level3)){ 7 level3term <- getGOTerm(as.character(level3[j]))$BP$level3[j] 8 leve...

...ckage), package = "") I think the call to getGeneric in namespaceImportFrom should use named arguments because impenv, an environment, will be assigned to the mustFind arg which is most likely not desired. An example where this seems to show up is in the check reports for GOstats: http://bioconductor.org/checkResults/1.9/gopher5-GOstats-checksrc.html Here's the snip from the check output (the results may have been updated in the meantime): * checking whether the name space can be loaded with stated dependencies ... WARNING Loading required package: methods...

...52 attached base packages: [1] "splines" "tools" "methods" "stats" "graphics" "grDevices" "utils" "datasets" [9] "base" other attached packages: Rgraphviz geneplotter XML GOstats Category hgu95av2 KEGG multtest xtable "1.11.9" "1.11.8" "0.99-8" "1.6.0" "1.4.1" "1.12.0" "1.8.1" "1.11.2" "1.3-2" RBGL annotate GO...

...uot; "1.15.0" "1.7.8" "1.7.3" "1.4-3" gcrma matchprobes biomaRt RCurl XML "2.7.3" "1.7.4" "1.9.21" "0.8-0" "1.6-0" GOstats Category Matrix lattice genefilter "2.1.13" "2.1.20" "0.9975-11" "0.14-16" "1.13.8" survival KEGG RBGL annotate GO "2.31" "1.15.12"...

...uot; "1.15.0" "1.7.8" "1.7.3" "1.4-3" gcrma matchprobes biomaRt RCurl XML "2.7.3" "1.7.4" "1.9.21" "0.8-0" "1.6-0" GOstats Category Matrix lattice genefilter "2.1.13" "2.1.20" "0.9975-11" "0.14-16" "1.13.8" survival KEGG RBGL annotate GO "2.31" "1.15.12"...

...uot; "1.15.0" "1.7.8" "1.7.3" "1.4-3" gcrma matchprobes biomaRt RCurl XML "2.7.3" "1.7.4" "1.9.21" "0.8-0" "1.6-0" GOstats Category Matrix lattice genefilter "2.1.13" "2.1.20" "0.9975-11" "0.14-16" "1.13.8" survival KEGG RBGL annotate GO "2.31" "1.15.12"...

...s provided for some difficult bug hunting when unit tests behaved differently than hand-run code even with set.seed(). The maintainer has been receptive to feedback and patches. You can look at the not-so-beautiful scripts and such we are using if you look at inst/UnitTest in: Category, GOstats, Biobase, graph Best Wishes, + seth =================== Discussion: After a bit more cursory use, it looks like RUnit is probably the right approach at this time (sorry Hadley!). Both RUnit and butler have a range of testing facilities and programming support tools. I support the above...

Greetings! The Bioconductor core group would like to announce the 5th release of Bioconductor, version 1.4. There are many new packages as well as several major upgrades and fixes in older packages, and users are encouraged to upgrade existing tools and check out the new packages. Release 1.4 is intended to be operated with R version 1.9.x, which can be obtained at CRAN

Dear All, I need to fetch GO ontologies for Homo sapiens with their mappings to corresponding Uniprot identifiers. I would be using this information to compare result from a clustering algorithm with existing protein complexes. This would be a test to check how the clustering algorithm accurately captures GO terms with respect to the known protein complexes. Can anyone suggest a simple workflow

...Clinical Variable GO A data package containing annotation data for GO GO.db A set of annotation maps describing the entire Gene Ontology golubEsets exprSets for golub leukemia data GOstats Tools for manipulating GO and microarrays. graph graph: A package to handle graph data structures graphics The R Graphics Package grDevices The R Graphics Devices and Support for Colours a...

...t;0.3-24" "1.4-2" "1.7.5" "1.6.1" xtable gcrma matchprobes biomaRt RCurl "1.4-3" "2.6.0" "1.6.0" "1.8.1" "0.8-0" XML GOstats Category genefilter survival "1.4-0" "2.0.4" "2.0.3" "1.12.0" "2.30" KEGG RBGL annotate GO graph "1.14.1" "1.10.0" "1.12....

I have recently upgraded to Ubuntu Gutsy and, for the first time, am using a 64-bit installation. After failing miserably to install R from source, not a problem for me in the past with a 32-bit install, I went the route of using the Debian Etch build. This went smoothly, but I am unable to update my numerous R and BioConductor packages, getting non-zero exit status errors on each package. Is