similar to: Memory problem ... Again

Hi, all; I know there has been a lot of discussions on memory usage in R. However, I have some odd situation here. Basically, I have a rare opportunity to run R in a system with 64GB memory without any limit on memory usage for any person or process. However, I encountered the memory problem error message like this: Error: cannot allocate vector of size 594075 Kb I got this error message while

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 have a question about how to increase my memory size, could someone answer it for me?? I am using Bioconductor in R to calculate gene expression values with mas5, dchip, and mas4. I have only 18 samples, all from Affymetrix U133A Plus 2 arrays, which has ~54,000 genes. My machine equipments are: CPU P4 3.0GHz, and 1GM RAM. Somehow when I was running mas5 in R, it always showed the error

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="") >

Sources for versions of R as far back as 0.65, I believe, are available on CRAN. You can try to compile from source. Andy > From: Qun Shi > > Hi, > > I'm trying to use the version of dchip combined with R to > analyze my data. > I need R version 1.6 which fits for dchip as dchip manual said. So I > would appreciate a lot if someone could tell me where I could

Googling for `rw1061.exe' turned up: http://www.cipic.ucdavis.edu/~dmrocke/Class/EAD289D/R/rw1061.exe Andy > From: Qun Shi > > Hi Andy, > > Thanks a lot for your promptly response. I searched the whole > web site, I > found the source code for version 1.6.X. Since I'm not a > computer person, > I don't how to compile it, but what I want is binary file

hi all i started recently using R and i found myself stuck when i try to analyze microarray data. i use the "affy" package to obtain the intensities of the probes, i have two CTRs and two treated. HG.U133A.Experiment1.CEL HG.U133A.Experiment2.CEL HG.U133A_Control1.CEL HG.U133A_Control2.CEL 1007_s_at 2156.23115 467.75615 364.60615 362.11865

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 all , I have one query. i have list of some .cel files. in my program i have to mention the path of these .cel files part of my program is, rna.data<-exprs(justRMA(filenames=file.names, celfile.path=*datadir*, sampleNames=sample.names, phenoData=pheno.data, cdfname=cleancdfname(hg18_Affymetrix U133A))) in the place of "datadir" i have to mention the character string of the

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

Dear R-help Hi, I'm Won. I try to do microarray normalization by R. I use justRMA function within affy package, got error about segment fault. I don't know why it happen. I attached error below. Please help me. Thank you. Cheers, Won ======================= OS : Redhat linux Cpu : intel xeon X5570 Memory : 26Gb & OS : Ubuntu Cpu : intel q6600 Memory : 8Gb

I use dChip and Affymetrix gtype to apply some genotyping functions to some microarrays data. Do you know if similar R functions exist? Thank you! Francesco ----------------------------------------------------------- Francesco Falciano, Ph.D. CINECA (High Performance Systems) via Magnanelli, 6/3 40033 Casalecchio di Reno (BO)-ITALY tel: +39-051-6171724 fax: +39-051-6132198 e-mail:

I have just spent a day trying to determine why I seemed to be unable to read a file of microarray expression results into R properly. The file was produced by the Dchip software developed by Li and Wong at Harvard's Department of Biostatistics. It contains rows of tab-delimited fields in the order Probe set identifier Probe set description Array 1 expression Array 1 call Array 2 expression

Dear all, I am a PhD student working with Affymetrix HGU133atag array for analyzing the Latin square experiment. I was trying to generate gene expression index for hgu133atag array for PDNN model. While extracting the chiptype specific data structure, I got the following error- > library(affypdnn) Loading required package: affy Loading required package: Biobase Welcome to Bioconductor

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

To whom it may concern, I am a student from Peking University, China. I am currently doing some microarray data analysis research with Bioconductor package of R. Problem arises when I try to import into R my dataset which contains 109 samples (total size more than 1.4 GB). The memory limit of R makes importing all the samples into one AffyBatch object a "mission impossible" for me.

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 am trying to upload into R 143 Affymetrix chips onto using R on the NIH Nimbus server. I can load 10 chips without a problem, however, when I try to load 143 I receive a error message: cannot create a vector of 523263 KB. I have expanded the memory of R as follows: R --min-vsize=10M --max-vsize=2500M --min-nsize=10M -max-nsize=50M (as specified in help in R). After running this command the