search for: gostat

Displaying 17 results from an estimated 17 matches for "gostat".

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2012 Jul 21
1
GOstats: get genes for corresponding enriched GO term
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,...
2008 Dec 10
0
FW: Kegg.db with GOstats
-----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 s...
2005 May 04
1
error with the function GOHyperG from GOstats package
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...
2006 Mar 10
1
Problem using GOstats package in R 2.2.1
...(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. Thank...
2006 Aug 11
1
[BioC] problem loading affycoretools (more details)
...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...
2004 Oct 12
2
Why I can't retrieve GO identifier correctly?
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 lev...
2006 Sep 22
1
Possible bug in base::namespaceImportFrom?
...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: method...
2006 Aug 31
1
problem with postscript output of R-devel on Windows
...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...
2007 Mar 23
1
can't load just saved R object "ReadItem: unknown type 65"
...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"...
2007 Mar 23
1
can't load just saved R object "ReadItem: unknown type 65"
...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"...
2007 Mar 23
0
can't load just saved R object using R-devel "ReadItem: unknown type 65"
...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"...
2007 May 09
4
Unit Testing Frameworks: summary and brief discussion
...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...
2004 May 17
0
Bioconductor 1.4 released
...ADES FOR RELEASE 1.4: =========================================== -- Proteomics (PROcess, gpls, apComplex) -- Array CGH (DNAcopy, aCGH) -- Cell cycle analysis (GeneTS) -- Packages for lab assay analysis and management (prada) -- Agilent arrays handling in limma -- Annotation tools (Resourcer, GOstat, goTools, ontoTools) -- Improved interfaces (limmaGUI, affylmGUI, webbioc, -- MAGE file processing (RMAGEML) -- affymetrix processing: many improvements, gcrma, affypdnn (probe-dependent nearest neighbors), affyPLM (probe-level models). -- marray (next generation of the depreciated marray...
2011 Sep 13
2
GO & Protein Complex Analysis for Homo sapiens
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
2007 Nov 02
0
loading installes package including all needed subpackages
...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...
2007 Feb 28
1
problem with help.start and ?somefunction
...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...
2007 Oct 30
6
trouble installing building packages from source using R 2.6.0 on Ubuntu Gutsy AMD64
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