similar to: Problem using GOstats package in R 2.2.1

Hi all, is it possible to modify the way a graph obtained through image(graphics) is filled, I mean starting filling the graphical matrix by row from the upper-left rather than by the lower-left cell... In many cases, it can be usefull to have a representation of the data spatialy corresponding to a real support, as it is the case with the function image(marray) from Bioconductor packages, which

-----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

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

Hi all, I am a relatively new R user... trying to put error bars (from SD values) on my data represented with barplot(). But I can't find any function or instruction to do so. Is there an easier way to do this than using segments() as I saw in an example in the R reference manual ? Then, can I define there graphical apparence ? Thanks for help. Regards Olivier BUHARD [[alternative HTML

Hi all, I know this is a stupid question, but I can't display a text file in a separate console window under a R session in X11 (gnome with MDK 9.2). I use R 2.0.0. When I enter : > file.show("/path/to/my/file/filename.txt" ,pager="gnome-terminal") the new window opens and then I just obtain the blinking cursor after the console prompt :-( I always obtain the same

I'm in the process of packaging R (and R modules) for future inclusion in Fedora Extras, and I've managed to get several hundred modules installed without issue, however, the GO metadata package is refusing to comply. Since I'm packaging this in rpm format, I can't use any of the automated functions for build, I've got to do it locally through R. The following steps work for

Do they open a file and load it into memory? I''m asking because it seems to take a long time opening a file but after it opens looping into the variable is REALLY fast, could someone explain me or tell me where can I find an explanaition on how this sort of things work? -- You received this message because you are subscribed to the Google Groups "Ruby on Rails: Talk"

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

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

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

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

Hi guys, Thanks for the great product. We've used dovecot for ages as our internal mail server and it works great! I've recently started using fetchmail 6.3.9 (with IDLE enabled) to download mail from our ISP (Pair networks). The ISP is running Dovecot 1.1.16. I am unable to get the info about the dovecot config at this time. The IDLE support in fetchmail allows us to deliver

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