similar to: A question about memory size

Dear all, I was trying to normalize a subset of affy data those transcribe are either P or M (called pm_filter). I am able to normalize pm_filter subset by using RMA method, however MAS5 is not working. For RMA method, I used the following commend: est<-rma(affydata, subset=pm_filter). Could any help me; how do I do this by using MAS5 method? Regards, Anup Som -- Dr. Anup Som,

Hello everybody, I am trying to use mas5 to normalize some array data and using mas5 and mas5calls. But I received these warning message. If anybody can explain the problem I would really appreciate that. Thanks in advance. background correction: mas PM/MM correction : mas expression values: mas background correcting...Warning message: 'loadURL' is deprecated. Use 'load(url())'

Hi all.. I'm very new R, and i'm analyzing microarray data using Bioconductor.. Recently i was given microarray data to analyze. The problem is whenever i run MAS5 presence calls algorithm, it throws an error saying NA/NaN/Inf in foreign function. How do i remove such NA/NaN/Inf's ?? I tried na.omit(dataframe) but stil problem exists. dimension of matrix (data) is 35556 7. >

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

Hi, I have built R (current development version) and BioConductor 1.7 with portland group compiler on a AMD Opteron. When I ran qc assessment on Affymetrix latin square data set, I got the following output, Loading required package: affy Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view,

Hi everyone, I'm quite new to LLVM *and doing a Q-learning *(*just a hobby*)* on register allocation for LLVM. RegAllocRL is based on* *RegAllocBase*,* RegAllocBasic and add some feature to implement Q-learning algorithm. * *I*’*ve currently run as MachineFunctionPass and things seem to work in simple case. In order to make progress on training*, *I have questions and want to get some

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 , 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

Is there R software available for doing approximate matching of personal names? I have data about the same people produced by different organizations and the only matching key I have is the name. I know that commercial solutions exist, and I know I code code this from scratch, but I'd prefer to build on some existing free solution if it exists. Unfortunately, the names are not standardized,

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

At first I would like to express the gratitude toward Oosting, J. and James MacDonal for their help solving the previous problem I posted on this forum. Now I have a new problem. I was trying to normalize set of microarray data on HGU133 paltform. I put all the HGU133A platform chips in one directory and all the other HGU133B chips on another directory. When I tried to normalized them using same

The Bioconductor development team announces release 1.2 of the Bioconductor packages for the analysis of genomic data. Bioconductor is an open source bioinformatics software project based on the R language. Version 1.2 features: ===================== * All packages from the 1.1 release are included. All current bug fixes have been applied, and most have been upgraded and provide enhanced

Hi Rich.. I'm now getting following logs after following your instructions.. libguestfs-test-tool ************************************************************ * IMPORTANT NOTICE * * When reporting bugs, include the COMPLETE, UNEDITED * output below in your bug report. * ************************************************************

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

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:

Hi Rich I'm noe getting the below logs after running libguestfs-test-tool.. SUPERMIN_MODULES=/lib/modules/3.8.13-rt9-QorIQ-SDK-V1.4 SUPERMIN_KERNEL=/boot/vmlinuz-3.8.13-rt9-QorIQ-SDK-V1.4 PATH=/bin:/sbin:/bin:/sbin:/usr/bin:/usr/sbin:/usr/local/sbin:/usr/local/bin SELinux: sh: getenforce: command not found guestfs_get_append: (null) guestfs_get_autosync: 1 guestfs_get_backend: direct

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

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