similar to: RBGL installation

Hi Christian, Chuck (and lists) It seems that the problem may be the strange behaviour of 'unstack' inside a function. See this thread in the R mailing list: http://tolstoy.newcastle.edu.au/R/help/04/03/1160.html Anyway, I got round the problem by using 'aggregate' instead of converting to a list and then tapply to sum values of metric. Probably more efficient as well. Thanks

Hello List I'm trying to calculate the median period (in months) of a set of time intervals (between two interventions). I have been playing with the lubridate package to create the intervals but I can't think of the right approach to get the median timeperiod. Toy code: library(lubridate) test <- c('08-04-22', '08-07-28', '09-03-02', '09-03-03',

Hello List I have a list question. I'm doing some data wrangling for a colleague and I have nested list in the following format: structure(list(MU10 = structure(c(0.80527905920989, 0.4350488707836, 0.455195366623, 0.565174432205497, 0.208180556861924), .Names = c("MU.16", "MU.19", "MU.21", "mean", "sd")), MU11 =

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)

Dear List I am trying to draw a heatmap using ggplot2. In this heatmap I have faceted my data by 'infection' of which I have four. These four infections break down into two types and I would like to reorder the 'infection' column of my data to reflect this. Toy example below: library(ggplot2) # test data for ggplot reordering genes <- (rep (c(rep('a',4),

Hi I've been trying to install RBGL and several other packages in gR task view on Fedora11 64 bit without success My guess is that it is due to boost (fedora is at boost 1.37 which is a few minor versions behind 1.40) and very recent g++ Has anyone managed to install the gR task view or RBGL in particular? Thanks Cheers Peter ======== [root at SPH-PH-428-04P ~]# gcc --version gcc (GCC)

Hi all, I was installing a package *RBGL* of bioconductor. However, I had some issues while installing it. I asked the devel group of bioconductor and they told me to consult this group. Here is my conversation with the bioconductor group related to the problem *Me->* I was trying to install the RBGL package using the following command biocLite("RBGL") However, I got the

I've just installed Debian Lenny and RBGL fails compilation with the following errors (sessionInfo() follows). * Installing *source* package 'RBGL' ... untarring boost include tree... ** libs g++ -I/home/mkimpel/R_HOME/R-patched/R-build/lib64/R/include -I/usr/local/include -IboostIncl -fpic -g -O2 -c bbc.cpp -o bbc.o In file included from /usr/include/c++/4.3/ext/hash_set:64,

Dear all, I am trying to run the function "lambdaSets" using the package "RBGL". This package uses another package "graph" which has been removed from the CRAN repository, but is available at the archive (http://cran.r-project.org/src/contrib/Archive/graph/). I installed the package from the R menu at "install packages from local zip files" (after

Hi all, I was installing a package *RBGL* of bioconductor. However, I had some issues while installing it. I asked the devel group of bioconductor and they told me to consult this group. Here is my conversation with the bioconductor group related to the problem *Me->* I was trying to install the RBGL package using the following command biocLite("RBGL") However, I got the

Hello list I have been given some Excel sheets with data laid like this: Col1 Col2 A 3 2 3 B 4 5 4 C 1 4 3 I was hoping to import this into R as a csv and then get the mean and SD for each letter in column 1. Could someone give me some guidance on best to approach this? Thanks Iain

Hi List I have a series of zip archives each containing several files. One of these files is called goCats.txt and I would like to read it into R from the archive. It's a simple tab delimited text file. pathToZip <- '/home/iain/Documents/Work/Results/bovineMacRNAData/deAnalysis/afInfection/commonNorm/twoHrs/af2hrs.zip' z <- unz(pathToZip, 'goCats.txt', 'r') zT

Hello list. I am hoping for some help with a relatively simple problem. I have a data frame arranged as below. I want to be able to count the occurrence of each gene (eg let-7e) by Experiment. In other words how many times does a given gene crop up in the dataframe. I tried table but couldn't work out how to get the output I want. I have also considered rearranging this data into a list (by

Hello list. I have a vector of values: eg > head(diff_mirs_list) [1] "hsa-miR-26b" "hsa-miR-26b" "hsa-miR-23a" "hsa-miR-27b" "hsa-miR-29a" [6] "hsa-miR-29b" and I would like to conditionally replace each value in this vector with a number defined in a dataframe: > fc ???????????? Probe ave.fc 1?????? hsa-let-7a?? 1.28 2?????

Hi. I have two vectors of gene expression for each of several days. I want to plot both vectors on the same plot for a visual representation of up versus down regulation. I've tried using add=T but that doesn't work. eg >plot(Day, gene1) >plot(Day, gene2, add=T) Any help would be appreciated. Iain

Hello everyone. How do I get R to ask users for data to be entered? Specifically I want to ask for a z score to be entered (the user would look this up in a table) and then use the entered data to compute a Dunn's post-hoc test (post kruskal.test). I've tried the "ask" function but it's not recognised - maybe I don't have to appropriate libary installed. A pointer

Hello List I'm moving this over from the bioC list as, although the problem I'm working on is biological, the current bottle neck is my poor understanding of R. I wonder if someone would help me with the following function. cumulMetric <- function(deMirPresGenes, deMirs){ ??? #need to match position of each miR in deMirPresGenes with its FC to form a vector of FC in correct order ?

Hello I have a Linux machine (Ubuntu 8.04 hardy, Gcc version 4.2.4 (i486-linux-gnu) currently running R 2.6.2. I'd like to upgrade to 2.10. First Question): What is the appropriate way to remove the old version of R? Part 2. After downloading r-base_2.10.0.orig.tar.gz and opening the archive. I ran the ./configure routine. It failed claiming that it could not find the F77 compiler. My

Some time ago I had difficulty installing RBGL with Ubuntu Hardy on R-2.7.0 and the problem was attributed to an with BGL. I got some very helpful advice and posted a script to fix the problem by hacking the RGBL source code: dateTue, Jan 15, 2008 at 2:16 PMsubjectRe: [R-sig-Debian] trouble installing building packages from source using R 2.6.0 on Ubuntu Gutsy AMD64mailing

Hello, I am having problems installing RSQLite under FC8. The error message seems to indicate Rversion.h and Rconfig.h are missing. To illustrate the problem, I have copied below the output shown when I first install R (binary distribution) and then try to install RSQLite. Because the problem does not occur when installing RSQLite with R under Windows I suspect the problem is perhaps due to my