similar to: R on Mac OS X 10.6 freezing up

Dear R Users, In the expresso function, which combination of these methods for data pre-processing (when using affymetrix oligo arrays) is the best: bgcorrect.metod = rma rma2 mas normalize.method = qspline quantiles loess pmcorrect.method = pmonly subtractmm mas summary.method = liwong avgdiff medianpolish mas There are many options within each method. I would appreciate a hint on the best

Hi Martin, In using the Cluster Package, I have results for PAM and DIANA clustering algorithms (below "part" and "hier" objects): part <- pam(trout, bestk) # PAM results hier <- diana(trout) # DIANA results GeneNames <- show(RG$genes) # Gene Names are in this object But

Dear R users, I am using the beadarray package. I am trying to upload raw bead-level data using these commands: ######################################################## library(beadarray) datadir <- ("C:/Computer_programs/R/beadarray/cecilia") targets = read.table("targets.txt", sep = "\t", header = TRUE, as.is = TRUE) BLData = readIllumina(arrayNames =NULL,

In using the NLME package (R 2.6.1 for Windows), I am having a problem in running an R script that used to run with no problems using a Linux OS in 2004. So I am wondering if during these last ~3 yrs we had major changes in the syntax of the NLME package that I am not aware. This is the R script: library(nlme) treat=as.factor(c(1,2,1,2,1,2,1,2)) mouse=as.factor(c(1,1,2,2,3,3,4,4))

Dear R-Help, I am using the function "topTable" from the LIMMA package. To estimate adjusted P-values there are several options (adjust="fdr" , adjust="BH") as shown below: topTable(fit, number = 10, adjust = "BH", fit$Name) I guess any of these options (fdr, BH, etc.) is using a default of FDR=0.05 which is quite conservative (i.e., very

Dear All, How to cite the PDF user's guide for the LIMMA package? This is not about how to cite the LIMMA package. Roger Roger L. Vallejo, Ph.D. Computational Biologist & Geneticist U.S. Department of Agriculture, ARS National Center for Cool & Cold Water Aquaculture 11861 Leetown Road Kearneysville, WV 25430 Voice: (304) 724-8340 Ext. 2141 Email: roger.vallejo@ars.usda.gov

Dear R-Help, I am using the LIMMA User's Guide 5 January 2007 PDF version. For the example show in Section 7.4 DIRECT TWO-COLOR DESIGNS (pgs. 33-34), I could not grasp the rationale in developing the contrast.matrix with these R statements (">" indicates the R command prompt): > contrast.matrix <-

Dear R People: I'm starting to think that I should just install from the binary, but here is my latest effort to install from source on a Windows 7 64 bit: c:\R64\R-patched>cd src cd src c:\R64\R-patched\src>cd gnuwin32/ cd gnuwin32/ c:\R64\R-patched\src\gnuwin32>set TMPDIR=c:\temp set TMPDIR=c:\temp c:\R64\R-patched\src\gnuwin32>make all recommended make all recommended

I'm running R 2.9.2 build 5464 on OS X 10.5.8. Having encountered memory allocation problems, I ran the problematic code in R64, the 64- bit version of the same build. When I attempt to load openNLP I receive the error message that the 32-bit version that I had been using does not run in R64. Assuming there is a 64-bit version, can I install and load it in R64 and, when I

Under MacOS I had R64 executive and it was clear. Under Ubuntu, which I do not have administrative rights to, there is only R executive. It seems that I can allocate more than 3GB of memory, however not everything seems to work the same/right as with R64 under MacOS. Pms.

This might be a very beginner question, but I'm looking for an example for something that I have never done. Suppose that I wanted to express actions with respect to lifted semantics of CPU instructions to an intermediate representation, BAP IL or LLVM IR. How might I go about providing a Backus Naur Form specification and then dynamically interpreting those lifted instructions by also

Hello! I'm using R-2.14.2 on a Windows 7 64 bit machine and I did the following: > install.packages("rJava",depen=TRUE) --- Please select a CRAN mirror for use in this session --- trying URL 'http://cran.sixsigmaonline.org/bin/windows/contrib/2.14/rJava_0.9-3.zip' Content type 'application/zip' length 745867 bytes (728 Kb) opened URL downloaded 728 Kb package

Hello: I have successfully installed both R and R64 for Apple OS X from CRAN plus GTK+2.14 and GGobi 2.1.8 from: http://www.ggobi.org/downloads I launch either R or R64 and try to install the rrgobi package and get (with R64) the following: R version 2.10.1 (2009-12-14) Copyright (C) 2009 The R Foundation for Statistical Computing ISBN 3-900051-07-0 R is free software and comes with

I'm running some code in R64 on a Mac OS 10.6.8 that calls a C program through the dyn.load() function. The code hangs after several days of computation, and I've having trouble locating the problem. Can anyone decipher this info from the error report, and tell me if this is a problem in R64, or in the C code? Thanks very much in advance. A few hints: "pa" is the name of the C

The USDA-Agricultural Research Service, Southeast Watershed Research Unit in Tifton, GA, is seeking a postdoctoral research associate for a full-time, 2 year appointment. The research associate will develop, calibrate, and validate a semi-empirical model for estimating cotton biomass from fields within the southeastern United States. Model development will involve the use of optical and radar

Hello, I am experiencing problems, when trying to assemble these two x86-64 Opcodes "add r64, imm32" "imul r64, r64, imm32" When having the most significant bit set for imm32, for example: "add rax, 0x80000000", "add rax, 0xffffffff", ... "imul rbx, rsi, 0x80000000", "imul rbx, rsi, 0xffffffff", ... The Error Message I receive is the

I'm new to Linux and Wine, so I need a little help. How do I run a program under Wine that performs an operation on a third file? IOW, I need to run the following DOS command line: C:\Program Files\Xprogram> mod.exe r64.dll How do I do this under Wine? I tried opening a terminal window and typing $ wine home\[restofpathname]\mod.exe r64.dll But I got an error saying it couldn't find

Hi, I have both R and R64 installed on Mac OSX 10.8 Mountain Lion (64-bit). When I run the command sessionInfo() from within Rscript, I get: R version 2.15.2 (2012-10-26) Platform: i386-apple-darwin9.8.0/i386 (32-bit) Is there a way to make Rscript point at the R64 rather than R (32-bit)? Thanks, Matt [[alternative HTML version deleted]]

Hi all, Not sure if this is the best list, please point me to a more appropriate list if necessary. Running Mac OSX 10.7.1 R version 2.13.1 Patched (2011-08-14 r56741) Copyright (C) 2011 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) I have a locally developed library (libmlalgs), which I am able to install via the command line:

Dear R People: I'm trying to compile R-2.15.0 on a 64 bit Windows machine. However, I'm getting the following error: c:\R64\R-2.15.0\src\gnuwin32>set TMPDIR=c:\temp set TMPDIR=c:\temp c:\R64\R-2.15.0\src\gnuwin32>make all recommended make all recommended make[1]: `MkRules' is up to date. make[4]: Nothing to be done for `svnonly'. installing C headers make[2]: Nothing to