similar to: FW: Kegg.db with GOstats

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, Tim [[alternative HTML version deleted]]

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 In fact first I tried this function with my locusId ' list (with

Dear all, This message is a kind of 'to be continued...' for that send by /Yu-An Dong,/ [BioC] problems with GO package data <https://stat.ethz.ch/pipermail/bioconductor/2006-February/011760.html>, last february. I've just installed R 2.2.1 on my computer (Windows based version) and downloaded Bioconductor available for this version via the graphical interface facility

I subscribed to the list and am awaiting a response. Thanks Best Regards, Roxane Eliff DADS/SEO AIX Administrator Office 301-763-7488 Mail Stop - 2K278B ----- Forwarded by Roxane B Eliff/DACMO/HQ/BOC on 01/21/2010 11:19 AM ----- From: Roxane B Eliff/DACMO/HQ/BOC To: samba at lists.samba.org <samba at lists.samba.org> Cc: Roxane B Eliff/DACMO/HQ/BOC at BOC Date: 01/19/2010 04:03 PM

Dear R users, I am trying to use the following code to make a barchar plot. The bars in the plot turn out to be a little narrow. Is there any way to modify the width of the bars? Thank you! library(lattice) scores = gl(2, 5, label=c('Sensitivity', 'PPV'), length = 100) sequences = gl(5, 1, label=c('Lemna minor', 'Dugesia japonica A', 'Gymnosporangium

Hi, It's unfortunate that with recent revisions of R 2.13 (this appeared in revision 54640, March 2), 'R CMD build' now removes empty dirs in the package. People might have good reasons for having empty dirs in their packages. For example, in Bioconductor, we have some tools to automatically generate annotation packages and those tools are implemented in software packages that use

Hi again, I have been playing around with the order of loading packages, and as far as I can tell, there's nothing specific with affycoretools that's causing my Rgui to crash (i.e., shuts down and the Microsoft 'please send error report' box pops up). Instead, it has something to do with the order & type of packages that are loaded that add items to the menu bar by

Hi, namespaceImportFrom in base/R/namespace.R has the following: fdef <- methods:::getGeneric(genName, impenv) The definition of getGeneric is in methods/R/RMethodUtils.R starts with: getGeneric <- ## return the definition of the function named f as a generic. ## ## If there is no definition, throws an error or returns ## NULL according to the value of

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

Hi I can't delete a file from a local server. I can list the file, however: # smbclient //WQS004/Comum -U user%pass -c dir\ '"Engenharia\PROJETOS LEGAIS 2014\PROJETOS 2012 A 2014\ARQUIVOS REVISADOS_07.2014\PROJETOS PLANTA JACAREI\FABRICA POLI\RICEFER_2808\PROJETOS\RO 04-400-01\92364 - Reator 4 m-¦ - Finalizador 6 m-¦.dwg"' Domain=[MYDOM] OS=[Windows 6.1] Server=[Samba

I have developed a problem with the postscript output of plot on Windows. My code still works properly with R 2.3 but, with R 2.4, the white text on red background does not show up. It does, however, show up when output is sent to the screen. Below is my code and sessionInfo. R version 2.4.0 Under development (unstable) (2006-08-29 r39012) i386-pc-mingw32 locale: LC_COLLATE=English_United

I have run into a problem loading a just saved R object using R-devel. I have been saving and loading this particular type of R object for a long while and never ran into this problem. I save, then immediately reload (to test save) and get "ReadItem: unnknown type 65". This error is reproducible after logout from server and restart of emacs and R. Below is my output and

I have run into a problem loading a just saved R object using R-devel. I have been saving and loading this particular type of R object for a long while and never ran into this problem. I save, then immediately reload (to test save) and get "ReadItem: unnknown type 65". This error is reproducible after logout from server and restart of emacs and R. Below is my output and

I am unable to load a just saved R object. Get message "ReadItem: unknown type 65" I am using R-devel and the problem is reproducible after logout and restarting R. Output and sessionInfo() below. Mark > setwd("~/Genomics/Experiments.Genomic/BB01/acb.shell") > local(save(affy.object.preprocessed, file ="affy.object.preprocessed.R" )) >

Hallo, I just installed all needed packages for my project on my PC. But I cannot load all at one time. I now want to load limma. How can I realize the following plan: I want to install for example limma inclusive all needed other sub packages (add-on). Can anyone tell me the corresponding command? Thanks, Corinna Here is the result of the command library(): Pakete in Library

I have samba 3.0.7 from the official RPMs working almost-perfect in our win2k3 domain with fedora core 2 ... except: smb mount works from the box in question as excpected for all but our two win2k3 domain controllers, one of which is our file server. shares mount from these but the permissions are as follows: drwxr-xr-x 2 root root 4096 Aug 26 23:46 floppy ?--------- ? ? ? ?

Hi all, I am going to be teaching a workshop next week using R and Bioconductor in one of our university's computer labs. They have recently installed R 2.4.1 for me, and I'm checking all my scripts. I just noticed that using the ?somefunction call to access the documentation for that function is not working. On my own PC, the ? call output changed between R 2.3 and 2.4; before it would

Dear Opus team, We are a PC, Tablets and Smartphones manufacturer in Brazil http://www.positivoinformatica.com.br/ . We were informed that the VP9 Video Codec will be added by Microsoft in the new versions of our contracts with them. We reseached this codec and sow that is developed by you and is royalty free. Would you please help me to check whether to sign any tipe of contract for the

Greetings - I'm finally finished review, here's what I heard: ============ from Tobias Verbeke: anthony.rossini@novartis.com wrote: > Greetings! > > After a quick look at current programming tools, especially with regards > to unit-testing frameworks, I've started looking at both "butler" and > "RUnit". I would be grateful to receieve real

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