similar to: cause 'memory not mapped'

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 have identical R.profiles and R_HOME directories set up on both my local machine and a remote linux cluster. To keep my libraries and R install separate, I use a site-library on both machines. The first line of my .Rprofile is: '.libPaths(new= "~/R_HOME/site-library") #tell R where site-library is' Until R-2.6.0 this was working fine on both machines, but since I have been

Dear R gurus, I have a function "goftests" that receives the following arguments: * a vector "x" of data values; * a distribution name "dist"; * the dots list ("...") containing a list a parameters to pass to CDF function; and calls several goodness-of-fit tests on the given data values against the given distribution. That is: ##### BEGIN CODE SNIP #####

I am trying to preprocess a large dataset of affymetrix data. Creating an affybatch is not possible with the computer I am running it on, so I have used the justRMA command to run RMA. I have read the affy document describing the justRMA command and the help documentation but I am unclear as to whether this command uses median polish after normalization. I assume this is the case but would like

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 all, What are current methods people use in R to identify mis-spelled column names when selecting columns from a data frame? Alice Johnson recently tackled this issue (see [BioC] posting below). Due to a mis-spelled column name ("FileName" instead of "Filename") which produced no warning, Alice spent a fair amount of time tracking down this bug. With my fumbling fingers

Dear R-helpers & bioconductor Sorry for cross-posting, this concerns R-programming stuff applied on Bioconductor context. Also sorry for this long message, I try to be complete in my request. I am trying to write a subset method for a specific class (ExpressionSet from Bioconductor) allowing selection more flexible than "[" method . The schema I am thinking for is the following:

Hi, I am having troubles with creating an eSet and would appreciate any help on the following problem. I am trying to create an eSet using the following code pd <- read.table(file="pdata.txt",header =TRUE,row.names=1); colnames(pd) <- c("type","tumor","time","id"); pdN <- list(type =

Hi, I'm using a command in bioconductor that seems to require a package called hu6800cdf. I've installed this properly but I still get the same error: Could not find array definition file ' hu6800cdf.qcdef '. Simpleaffy does not know the QC parameters for this array type. See the package vignette for details about how to specify QC parameters manually. I've tried specifying

Hello, I have a problem with read.affy.mixed function. I want to read in together a set of CEL files from chip types Affymettrix HGU133A_2 and HGU133_Plus_2. I have my files to be read in in one directory together with a white space delimited file describing them (covdesc). In this directory I give a command: > merge <- read.affy.mixed() Error in merged[[i]] : subscript out of

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

Dear R-help, Hi I've got data table with variation and freqeuncy. I don't know how to get mean and sd. Please help me. Cheers. ========== variation frequency 0.503 79930 0.174 291140 -0.444 95916 -0.731 11451 0.453 102899 0.596 46133 -0.295 204859 0.013 390121 0.311 187552 -0.085 378902 -0.633 28164 0.175 291411 0.611 41903 0.318 183254 -0.661 22580 0.149 312574 0.594 46903 -0.557

Dear Community, I am very new to the world of Linux and R and I have stumbled upon a problem that I cannot seem to resolve on my own. Here is the relevant background: I am working on a 64-bit Linux Fedora Core 6 OS. I using R version 2.5.1. I have 3.8 Gb of RAM and 1.9 Gb of swap. As I see it, there are no restraints on the amount of memory that R can use imposed by this particular OS build.

Hello, I am using the following code to plot an MVA plot. library(affy) library(Biobase) library(limma) library(gcrma) pd<-read.phenoData("Clk.targets.2.txt",header=TRUE, row.names=1,as.is=TRUE,sep="\t") Data <- ReadAffy(filenames=pData(pd)$FileName,phenoData=pd) Print(Data) eset <- gcrma(Data) write.exprs(eset,

Hi, Can anyone help me of the affylmGUI package, I can't get it work and searched for google but can't find any proper solutions. I get the error information each time when I load my cells files, which are shown in the following links. ------------- http://clarezoe.googlepages.com/1.png http://clarezoe.googlepages.com/2.png http://clarezoe.googlepages.com/3.png ------------- Errors also

Dear listers, After activating the name space for my bioconductor package (prada) I successfully ran R CMD check. However when loading the package in R and running the examples the imported function brewer.pal from package RColorBrewer is not found. I can directly call brewer.pal from the RColorBrewer name space typing RColorBrewer::brewer.pal, but it is not imported into my prada name space. When

Dear listers, After activating the name space for my bioconductor package (prada) I successfully ran R CMD check. However when loading the package in R and running the examples the imported function brewer.pal from package RColorBrewer is not found. I can directly call brewer.pal from the RColorBrewer name space typing RColorBrewer::brewer.pal, but it is not imported into my prada name space. When

Hello. By way of background, I am running out of memory when attempting to normalize the data from 160 affymetrix microarrays using justRMA (from the affy package). This is despite making 6 gigabytes of swap space available on our sgi irix machine (which has 2 gigabytes of ram). I have seen in various discussions statements such as "you will need at least 6 gigabytes of memory to normalize

Hello, I'm wondering how I can merge two featuresets into one. My dataset is two sets of microarray data and it looks like followings: > rawData $v1 TilingFeatureSet (storageMode: lockedEnvironment) assayData: 2197815 features, 59 samples element names: channel1, channel2 protocolData rowNames: LT290677RU_D1_2011-02-16 LT286300LU_D1_2010-07-24 ... LT003990RU_D1_2010-11-04 (59

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