similar to: .First.lib doesn't appear to be running after calling lib rary()

Hi - so I've dusted off the C bits of my brain and gotten a library written for my package... It passes R CMD check ok, and I've put a file called '.First.lib.R' in the pacakge's 'R' subdirectory. Its permissions are 644. It says: .First.lib <- function(lib,pkg) { library.dynam("foo",pkg,lib); require(affy,quietly=TRUE); } I build and INSTALL

Hi, I've got a quick question about file permissions and packages... I'm creating my own package, and am having problems with its vignette not being seen when I install it into R... As I understand it, the permissions of the source tree should be as follows: o Directories - drwxrwxr-- o Files - -rw-r--r-- Everything builds and runs through 'R CMD check' fine with

Hi, Forgive a very basic question... I need to take two lists-of-lists, and apply a function to each pair of elements in the lists to return a single list... For example l1 <- list(1:5,6:10,2:15) l2 <- list(1:8,4:12,1:19,4:20) I could easily do an lapply across each of them, but is there a function that does a sort-of pairwise-apply across both together? Does anybody know of a good

Hi, I decided to upgrade to 1.8 today... :-) Anyway, we are writing our own package that is dependent on a bioconductor library - 'affy'. I've checked and when I fire up R, library(affy) behaves as expected... so it all seems to be installed and OK... In the DESCRIPTION file in my package source I have the line: Depends: affy When I run R CMD check simpleaffy I get to: ... *

Hi, I have built R (current development version) and BioConductor 1.7 with portland group compiler on a AMD Opteron. When I ran qc assessment on Affymetrix latin square data set, I got the following output, Loading required package: affy Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view,

My machine has 8GB memory. I had quit all other programs that might take a lot of memory when I try the script (before I post the first message in this thread). The cdf file is of only 741 MB. It is strange to me to see the error. On Mon, Dec 28, 2009 at 2:38 AM, Wolfgang Huber <whuber at embl.de> wrote: > Dear Peng Yu > > how big is the RAM of your computer? You could try with

Hi, We're looking for a number of people to join our group (Applied Computational Biology and Bioinformatics -- ACBB) and applying state of the art techniques (see for example, xmap.picr.man.ac.uk) to integrate, analyse and interpret datasets arising from the latest generation of microarrays (including exon, SNP and tiling arrays), quantitative mass-spectrometry and next generation

Hi, I hope you don't mind me posting this to the list: We are seeking a postdoctoral scientist to join the Applied Computational Biology and Bioinformatics group at the Paterson Institute for Cancer Research. The role will be to develop novel approaches for the analysis of high throughput genomic data, such as those arising from Affymetrix microarray experiments. We are an

I am getting the following error in my script. I am very very new to R and have obtained this script from another person. #read file in (dummy data) starburst.plot<-function(affy.fold, affy.FDR)(ifelse( ((affy.fold) >=0), -1*log10(affy.FDR), 1*log10(affy.FDR))) starburst.plot<-function(meth.fold, meth.FDR)(ifelse( ((meth.fold) >=0), -1*log10(meth.FDR), 1*log10(affy.FDR))) At my next

Hi, We are seeking a postdoctoral scientist to join the Applied Computational Biology and Bioinformatics group at the Paterson Institute for Cancer Research. The role will be to develop novel approaches for the analysis of high throughput genomic data, such as those arising from Affymetrix microarray experiments. We are an interdisciplinary team that brings together skills in computer

Dear all, we have an exciting PhD position applying HPC to the analysis of large scale cancer datasets. The post will suit an applicant from a strong computational background who wishes to apply their knowledge to help develop a better understanding of the processes that control how tumours develop. Details below:- High Performance Computing applied to cancer research: Computational analysis of

Hello, I am trying to install affy package in R as follow: >R CMD INSTALL -l lib ~/rstuffs/affy_1.4.32.tar.gz Then I get an error at the end: Warning message: There is no package called 'Biobase' in: library(package, character.only = TRUE, logical = TRUE, warn.conflicts = warn.conflicts, [1] "ProgressBarText" [1]

Hello all, I am trying to make a genome association plot for p-values related to SNPs and was fortunate to find that R contains a package that produces Manhattan plots which is what's preferred for my current project. The function mhtplot() is found in the 'gap' package which I installed in R 2.11.1 on Windows. I thought I'd test out the function first with the examples they

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

Begin forwarded message: > From: Barry Leiba <barryleiba at computer.org> > Date: 20. marraskuuta 2012 2.44.51 UTC+2.00 > To: imap5 at ietf.org, imapext at ietf.org, imap-protocol at u.washington.edu, imap-use at u.washington.edu > Subject: [imapext] News about Mark Crispin > Reply-To: imap5 at ietf.org > > Everyone here knows Mark Crispin -- or at least knows who he

Hi, I have been using the prcomp function to perform PCA on my example microarray data, (stored in metric text files) which looks like this: 1a 1b 1c 1d 1e 1f ...................................................4r 4s 4t g1 1.2705 1.2766 ...........................................................2.0298 g2 0.1631

Hi R-ers, I am struggling with my x-axis in a association plot. What I would like is to place the labels of the x-axis between the tick markers and normally the labels are printed at the place where the tick marker is placed. I don???t want to move the tick marker (it gives the switch between one chromosome and the next) but I just want to put the chromosome number in between the

Hi, I've got a quick question about what happens when indexing into matrices with a single column. I was wondering if anyone can help ... For example: > x <- matrix(1:10) > y <- cbind(x,x) > x[4:6,] [1] 4 5 6 > y[4:6,] [,1] [,2] [1,] 4 4 [2,] 5 5 [3,] 6 6 > class(x[4:6,]) [1] "integer" > class(y[4:6,]) [1] "matrix" It seems that R

Hi, all. Something strange happened to my ESS. I use Mac OS X. When R is used in stand alone mode, it recognizes external libraries like "affy", "e1071" etc. However, when R is invoked through ESS in Emacs, it produces errors like: Error in library(affy) : There is no package called 'affy' Interestingly, I remember I successfully used these libraries through ESS in