similar to: [Q] raw -> gpr in aroma package

Dear R-users: I am runing R 1.6.2 with Windows XP. I try to calculate Pearson correlation and Spearman correlation of any pairwise columns of 8000 x 80 data matrix with missing values and randomize the matix 1000 times and calculate this two correlations again. The code bellow for Pearson is working fine but for Spearman got the error bellow for randomized data matrix and R console is stop

I don't know if this is the correct forum to ask the following question; however, when I search the aroma.affymetrix discussion group, it suggested that I should posted the question to r-help. Here it goes. I followed the instructions on aroma.affymetrix trying to install the packages; following are the steps: > install.packages(c("R.oo", "R.utils"),

Hi, FYI, I just notice that on Windows (but not Linux) it is orders of magnitude (below it's 50x) faster to serialize() and object to a temporary file and then read it back, than to serialize to an object directly. This has for instance impact on how fast digest::digest() can provide a checksum. Example: x <- 1:1e7; t1 <- system.time(raw1 <- serialize(x, connection=NULL));

Hi List, I'm trying to install aroma.affymetrix, which depend on many packages, affyio is one of them. The task is done on 32-bit Linux without problem. The same task was done on Solaris 9 with R-2.5.1 without problem. Following is the error message when installation affyio. I did try to put a file stdint.h I got from the web in the path, but got more error messages. Jun root@biostatsun1

Hi Accesses the $new method for a class defined in a package fails if the methods package is not loaded. I have created a test package with the following single code file: newTest <- function() { cl <- get("someClass") cl$new } someClass <- setRefClass("someClass") (This is similar to code actually used in the testthat package.) If methods is not loaded,

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Hello, I wonder if it is unwise to name a bundle the same as one of its packages. For instance, I now have a huge package called 'aroma' that I basically want to split up in several smaller packages, say 'aroma.core', 'aroma.io', 'aroma.explore', 'aroma.trial', 'aroma.deprecated' etc, which simplifies maintenance but also the overview. For

Dear R users, I'am using marray and Limma packages to analyze genepix output. 1) how can I filter bad spots from my data (data contains 3 types of bad spots). my experiment contains 12 samples and the bad spot are not associated to the same probes 2) how can I remove control probes from my data ? I'm sorry, i'm new with R and I can't find answer in packages doc. best regards,

Hello. I use Linux 2.0.30(Red Hat) and Samba 1.9.16p. Clients are Win95, NT Workstations and Servers. I use Linux like printserver and bridge. And I have problem with my printer HP LaserJet 4MV with JetDirect card. It print 1 test page( or another 1 page) and print after it second page: User: root Host: LINUX Class: LINUX

Dear whom this may concern, I am having problems running R under windows XP. I can source files and get all the functions loaded, but when directing it to a file to carry out analyses it comes up with an error message. I am using R for analyses of gpr files generated from microarray slides using Axon genepix 2000. I hope you have a solution to my problems. Kind regards, Jan Bart Rossel (PhD

Hi, I'm trying to write a function in C for implementation with .Call. When compiling using R CMD SHLIB characters seem to be added to the function name. Here's the complete C code from the file summariseMCMC.c: #include<R.h> #include<Rdefines.h> #include<Rinternals.h> void summariseMCMC(SEXP data) { PROTECT(data=AS_NUMERIC(data)); UNPROTECT(1); } Then

Dear all, I have a question about limmaGUI that is usually run in R environment. My problem is loading data into the programm. I have 6 gpr files that apparently are not compatible with limma. Everytime I'm trying to load the data (including a RNA targets file, an error appears:Error reading files. that I'm not sure,but seems to have something to do with the format of my files

I've tried to run demo of Hard Reset and it has two big problems on Wine. First is that mouse isn't working. You get input only from keyboard but that can be solved with raw input patch. I used the one that is working with Deus Ex: Human Revolution: http://dl.dropbox.com/u/6901628/raw2.patch but second is much worse. Basically almost all of the textures aren't rendered. It starts

Full_Name: Henrik Bengtsson Version: 1.5.1 OS: WinMe Submission from: (NULL) (217.210.0.243) In the Perl script $R_HOME/bin/check there is a bug under the section "Check R code for syntax errors" where the 'Rfiles <- c(...)' is build up. If there are too many files in @Rfiles the source code line generated will be too long and weird things will happen, e.g. strange

During installation of a package, Makevars/Makefile in src/ is processed. I've always considered the purpose of this for compiling native code. Is that it's solely purpose, or is it alright to use it also for non-code compilation purposes, e.g. building inst/ subdirectories on the fly? If not, are there other means to create non-static inst/ subdirectories during installation? The

FYI, I'm sure the following is a temporary issue, but in case it slips through, I want to raise it here. On Windows 7 64-bit, running Rcmd check on R devel gives: * using R version 2.13.0 Under development (unstable) (2011-02-11 r54330) * using platform: x86_64-pc-mingw32 (64-bit) * using session charset: ISO8859-1 * checking for file 'aroma.core/DESCRIPTION' ... OK * this is

I'm rather frustrated in trying to run the examples on the robustSmoothSpline. No matter what packages I load, I still come up with the error as follows. Error: could not find function "robustSmoothSpline" Am I missing something?

Hi, I got an interesting programming challenge: How do you inspect an object which is assigned via delayedAssign() and that throws an error as soon as it is "touched" (=the value is evaluated)? Is it possible? MINIMAL EXAMPLE: $ R --vanilla > delayedAssign("foo", stop("Hey!")) (If you find this minimal example silly/obvious, please skip down to the real

Does R have a comparison operator similar to the Like function, for example: a<-"Is a Fish" b<-"Fish" if(b in a){c<-TRUE} Michael R Howard Micron Technology Inc. Boise ID. Fab C Engineering Software (FCES) Software Engineer

Hello, When I launch a script under windows it does not display sequentially my cat calls or maybe the console is not refreshed at every line of my script. For instance with that code cat("\n\n================== IMPORT DATA FROM FILE ===================\n\n") fileschosen <- choose.files(caption="Select gpr files", filters = matrix(c("genepix