similar to: GOstats: get genes for corresponding enriched GO term

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

-----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

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

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

Hi Andy, I know this topic has been discussed before on the R-help, but I was wondering if you could offer some advice specific to my application. I'm using the R random forest package to compare two classes of data, the number of cases in each class relatively low, 28 in class 1 and 9 in class 2. I'd really like to use R environment to analyze this data, however I'm finding it

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 List I have data in the following form: Gene    TFBS NUDC     PPARA(1) HNF4(20) HNF4(96) AHRARNT(104) CACBINDINGPROTEIN(149) T3R(167) HLF(191) RPA2     STAT4(57) HEB(251) TAF12     PAX3(53) YY1(92) BRCA(99) GLI(101) EIF3I     NERF(10) P300(10) TRAPPC3     HIC1(3) PAX5(17) PAX5(110) NRF1(119) HIC1(122) TRAPPC3     EGR(26) ZNF219(27) SP3(32) EGR(32) NFKAPPAB65(89) NFKAPPAB(89) RFX(121)

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 have a data.frame with 294 columns and 211 rows. I am calculating correlations between all pairs of columns (excluding column 1) and based on these correlation values I delete one column from any pair that shows a R^2 greater than a cuttoff value. (Rather than directly delete the column all I do is store the column number, and do the deletion later) The code I am using is: ndesc

Hello, I am exporting a graph in "gml" format from igraph 0.5.5. When I open the file in Cytoscape v.2.7 I can't map the color attribute that I assign to the graph when I export it from igraph. Could anyone help me in this? Thanks. -- Warm Regards, Sandeep Amberkar BioQuant,BQ26, Im Neuenheimer Feld 267, D-69120,Heidelberg Tel: +49-6221-5451354 [[alternative HTML version

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

Hello all, I would like to introduce our group's new bioinformatics package to you: pathfindR <https://cran.r-project.org/package=pathfindR> This tool is designed to improve pathway enrichment analysis by firstly identifying active subnetworksin differential expression/methylation data using a protein-protein interaction network. It then performs pathway enrichment analysis

Hello all, I would like to introduce our group's new bioinformatics package to you: pathfindR <https://cran.r-project.org/package=pathfindR> This tool is designed to improve pathway enrichment analysis by firstly identifying active subnetworksin differential expression/methylation data using a protein-protein interaction network. It then performs pathway enrichment analysis

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

Hello Everyone! This is my first post to the mailing list so please forgive me if I am a bit deflected from the general format of this mailing list posts. Since I need help in this matter urgently, I would cover up any of my mistakes in posting later. That said, I have a problem in merging 2 graphs that have common nodes between them. I have a graph G1, that have nodes N1 and edge set E1 and

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'm having problems with this example, it is posted with reproduceable code below, both with the normal 0-6 scale and the desired 3-6 scale (with bars removed). How can I get the graph to have the desired 3-6 scale without removing the bars. Thanks! #Data

Hi, I'm trying to use the XML-RPC client in the SSOAP package to connect to a service that I have created. From other languages (Perl, Python, Ruby) this is not a problem but the SSOAP client gives the following error: Error in .XMLRPC("http://localhost:9000", "Cytoscape.test", .opts = list(verbose = TRUE)) : Failed to parse XML-RPC request: Content is not allowed in

A while ago someone asked about a low-pass filter for oggenc and was told to get AFsp and filter outside of Oggenc. Well, I got it, and am totally lost (It's way more complicated than SOX) so now can anyone briefly describe what type of filter I should set up (FIR, IIR, all-pole), why one is better than the other, and if you have filter coefficient files lying around (lowpass, 19 or 20 kHz