similar to: R cannot find the path on my mac

Hi I am trying to install a package (bioconductor) but every time I try to install it I get this message: source("http://bioconductor.org/biocLite.R") Warning in install.packages("BiocInstaller", repos = a["BioCsoft", "URL"]) : 'lib = "C:/Program Files/R/R-3.0.0/library"' is not writable Error in

Hello, I have an input file: http://r.789695.n4.nabble.com/file/n3700031/testOut.txt testOut.txt where col 1 is chromosome, column2 is start of region, column 3 is end of region, column 4 and 5 is base position, column 6 is total reads, column 7 is methylation data, and column 8 is the strand. I would like a summary output file such as:

Hello, I have an R script that I use as a template to perform a task for multiple files (in this case, multiple chromosomes). What I would like to do is to utilize a simple loop to parse through each chromosome number so that I don't have to type the same code over and over again in the R console. I've tried using: for(i in 1:22){ etc.. } and replacing each chromosome number with

Hi, I want to use reutils to obtain the accession numbers of a query search in character format. When I use efetch, the accession number isn't in a character format, and I'm not sure if the number is accurate, because I get the error: Error in file.exists(destfile) : object 'destfile' not found This is what I tried: UIDs<-esearch( "Methylation" ) accession_numbers

Dear List, I have been trying to use p.adjust() to do BH multiple test correction and have gotten some unexpected results. I thought that the equation for this was: pBH = p*n/i where p is the original p value, n is the number of tests and i is the rank of the p value. However when I try and recreate the corrected p from my most significant value it does not match up to the one computed by the

Hi Bert and David, Thank you so much for willingness to spend some time on my problem!!! I have some statistical knowledge (going to get a master in applied statisitics), but do not have a chance to purse a phD for statistics, so I am always be careful before starting to do analysis and hope to gather supportive information from real statisticians. Sorry that I did not tell more info about

David: I believe your response on SO is incorrect. This is a standard OFAT (one factor at a time) design, so that assuming additivity (no interactions), the effects of drugA and drugB can be determined via the model you rejected: For example, if baseline control (no drugs) has a response of 0, drugA has an effect of 1, drugB has an effect of 2, and the effects are additive, with no noise we

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 actually have two questions regarding the same script: ################################################# data <- vector('list', 24) splc <- vector('list',24) df.summ <- vector('list',24) for (i in 1:length(chrData)) { data[[i]] <- read.table(file=paste('chr',i,'.nonCG.covered.out',sep=''), header=F)

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, I have a set of templates creating some files for me. All data on my site is encoded using iso-8859-1. Now I want to save the text in the file using utf-8. I have tried using iconv, but whenever I have the require "iconv" statement in my model, there is some error happening in the model and the model doesn''t get loaded (not sure how to debug that). What approches to

Hi ! My mongrel just starting spitting out these nice lines: The error occured while evaluating nil.accept. TELL ZED HE''S A MORON. !!!!!! UNHANDLED EXCEPTION! You have a nil object when you didn''t expect it! Not sure what happened or why, but just FYI: Zed, you are a moron :-) Happy holidays! Gitte Wange

Hello, I have an interessting problem, I''m not sure how to solve :-) I have the name of a model in a variable like this: My model is called Article My var contains "Article" Now - How do I get the model class, so I can call Article.find, Article.new etc ... ? Greetings, Gitte Wange

Hi All: Greetings, and best wishes from the festive times here at Kolkata, India -- the time of Durga Puja celebrations. I seek your advice as I try plotting lines for my data. The problem: I have created a dataframe that looks like this (name: myFrame): lowest second third fourth highest significance INAS 0.107 0.115 0.123 0.115 0.166 0.000 MMA 0.091 0.107 0.115

Hi! The ruby installation on my FreeBSD-6 box have been upgraded from 1.8.2 to 1.8.4 by accident. And now all my rails have stopped working. I can''t produce any cool debug info since I have none. running script/ server just coredumps. Running the sites through apache isn''t an option since apache won''t start (get lots of these in my log: [Thu Feb 09 10:38:19

Hi! I''m trying to use a primary key made up of two columns in my model''s table. But looking at the docs, it looks like ActiveRecord only supports using one field as primary key. Can anyone point me in a direction of this or verify that it''s not supported? Greetings, Gitte Wange

For a project I''m working on I''m hoping to be able to have both discussion and announce-only e-mail lists. Does anybody have any recommendations about good existing mailing list apps that could be integrated with a rails app? Does anybody have any experience using ActionMailer as the basis for a mass mailer? Does it perform well enough to make it feasible? Thanks! -- Dan

Hi, I have good this cool challenge from my boss on developing a very simple cms-like system to publish articles within. The caveat is that he wants to have multi-lingual content. At first I thought RoR would be perfect for the assignment but right now I''m not so sure. My first attempt involved creating a table for each model/languagde like this: articles_en articles_dk articles_de

Hello, I''ve spent a couple of hours now searching for (what I thought) was pretty straightforward. I''m using mongrel together with RoR and need to execute a .rb file located in my public folder (cgi style). But mongrel just can''t do that out-of-the-box - or am I missing something? I really don''t get how I''m supposed to configure mongrel for this

CRAN (and crantastic) updates this week New packages ------------ * bisectr (0.0.2) Maintainer: Winston Chang Author(s): Winston Chang <winston at stdout.org> License: GPL-2 http://crantastic.org/packages/bisectr Tools to find bad commits with git bisect * CUMP (1.0) Maintainer: Xuan Liu Author(s): Xuan Liu <liuxuan at bu.edu> and Qiong Yang <qyang at bu.edu>