similar to: Configuration of memory usage

Happy new year to all; A few days ago, I posted similar problem. At that time, I found out that our R program had been 32-bit compiled, not 64-bit compiled. So the R program has been re-installed in 64-bit and run the same job, reading in 150 Affymetrix U133A v2 CEL files and perform dChip processing. However, the memory problem happened again. Since the amount of physical memory is 64GB, I think

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

Full_Name: Eric Libby Version: 2.1.1 OS: OS Tiger Submission from: (NULL) (65.93.158.117) I am trying to analyze microarray data of 42 human arrays. I typed in the following instructions: library(affy) Data <-ReadAffy() eset <- expresso(Data, normalize.method="invariantset", bg.correct=FALSE, pmcorrect.method="pmonly",summary.method="liwong") And I get some

Hello Everyone, I am writing programs in R from 7 months and I am able to solve most of the errors/issues except for this current post. My Task is to read a Microsoft Excel file(textE_to_affy.csv) which contains the Microarray Expression Values collected from the Illumina Microarray experiment. These collected intensity values need to be normalized(Rank Invariant Normalization) by using the R

Hi!I'm doing a little data importing from .cel files, > setwd("/home/mandova/celfiles") > mydata<-ReadAffy() Error in sub("^/?([^/]*/)*", "", filenames, extended = TRUE) : unused argument(s) (extended = TRUE) Then I tried > filenames<-paste("GSM",c(seq(138597,138617,1)),".cel",sep="") >

Hi, I have a question concerning the analysis of some affymetrix chips. I downloaded some of the data from GEO GSE11324 (see below). In doing so I'm stuck after I identified the probesets with significant changes. I have problems in assigning probeset specific gene names as well as getting the genomic coordinates. Furthermore I have no clue how to deal with the fact, that most genes have

Hi This is a question prompted by the mac version of R, but as I see it, it should have broader interest. These days the CRAN Mac binary per default compiles every package for two architectures. First i386 and then ppc. In between the two compilation runs, any object files in pkgname/src is removed. This cleanup is necessary since otherwise Make would not recompile the object files

Full_Name: Edward J. Oakeley Version: 1.7.1 OS: Windows XP Submission from: (NULL) (212.47.183.3) This bug occurs when using the (D)COM server to connect to the "expresso" command of the Bioconductor Affy package. It may be a bug of R, (D)COM or Affy ut I will report it here anyway as it feels like an R bug. The Affy package when invoked will read a series of large (10Mb) text files

I've looked through all of the posts about this issue (and there are plenty!) but I am still unable to solve the error. ERROR: cannot allocate vector of size 455 Mb I am using R 2.6.2 - x86_64 on a Linux x86_64 Redhat cluster system. When I log in, based on the specs I provide [qsub -I -X -l arch=x86_64] I am randomly assigned to a x86_64 node. I am using package GenABEL. My data (~ 650,000

[Please CC me in any replies as I am not currently subscribed to the list. Thanks!] Dear all, I did a bit of searching on the question of large datasets but did not come to a definite conclusion. What I am trying to do is the following: I want to read in a dataset with approx. 100 000 rows and approx 150 columns. The file size is ~ 33MB, which one would deem not too big a file for R.

I am trying to sort out a configuration problem with y slave servers, more on that in a following message, but while I was examining the system log on one of those servers I saw this: Nov 3 12:30:43 inet04 named[18110]: client 174.88.12.107#60136: query (cache) 'www.soundunwound.com/A/IN' denied Nov 3 12:30:43 inet04 named[18110]: client 174.88.12.107#60140: query (cache)

Hello, I have noticed that the memory usage inside an R session increases as more and more objects with unique names are created, even after they are removed. Here is a small reproducible example: > gc() used (Mb) gc trigger (Mb) max used (Mb) Ncells 531720 14.2 899071 24.1 818163 21.9 Vcells 247949 1.9 786432 6.0 641735 4.9 > > for (i in 1:100000) { + name <-

Hey guys, I used "script/generate controller admin/event" How do I link to the views and the controller when it''s inside a directory. I tried <%= link_to "some link", :controller=>"event",:action=>"index" %> <%= link_to "some link", :controller=>"admin/event",:action=>"index" %> <%=

Hi, Finally I managed to build (as ordinary user in my home dir) 1.0b2. (remember, I had problems with db-ldap.h disappeared after compile) What is the (simplest and) safest way to shut down dovecot on the live server and replace the running 0.99.14? I run OpenBSD 3.7 on Sparc. The last step would be 'make install', of course. To shutdown dovecot the last time I resorted to kill

I have been studying Tom''s configuration at: http://www.shorewall.net/myfiles.htm -and- http://www.shorewall.net/NAT.htm I am using SBC as an ISP and also have 5 "real" IP addresses and because of other issues, have to re-do my set-up. If I have a block at .120/29 assigned to me, what SBC does is give you 5 usable addresses, in my case .121 is the SBC modem/router and

Hi When I'm using clang 3.1 with the isysroot argument, it doesn't seem to pick up header files from the directory I'm passing through the command line: > $ clang -isysroot/myownheaders -v foo.c -c -o foo.o > clang version 3.1 (tags/RELEASE_31/final) > Target: i386-pc-linux-gnu > Thread model: posix > "/usr/bin/clang" -cc1 -triple i386-pc-linux-gnu -emit-obj

Hi folks, I installed a new samba-PDC-server (dual athlon, raid,...) with Redhat 9++ and samba 2.2.8a from rawhide. I copied all (?) configfiles (/etc/samba/*) from my old server an adjusted some shares. The old server (RH 8, Samba 2.2.6, single PIII) was working for a couple of month without a probelm; I could create mashineaccounts on the fly from windows 2K and XP Pro, profiles and

On 03/04/2012 02:32 PM, Harel Cain wrote: > Thanks, but I'm not sure I understand. I see no such flag in clang 2.9 > nor couldn't I find any mention of it. What does it do? It's called -mllvm. You can use it like this. clang -mllvm -vectorize ... Cheers Tobi

I have tried to invoke a transformation/optimization pass using -mllvm, without success. I might be missing something. For example I have a shared/dynamic library which contains LLVM passes. I used to invoke them with llvmc like this: >>*llvmc mycode.c -o mycode.o -c -opt -Wo,=-load,libFoo.dylib,-Foo* Can this style of optimization be executed using -mllvm argument? Thx, PMon On Sun,

I'm do looking for the features the isysroot gives. I have "/myownheaders/usr/include" and "/myownheaders/usr/local/include" folders (they contain the actual header files). Again, the strange that gcc seem to be working with it. In the mean time I've found this (http://lists.cs.uiuc.edu/pipermail/llvmbugs/2011-December/021136.html), isn't it related? > From: