similar to: RAM, swap, Error: cannot allocate vector of size, Linux:

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

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

Hello! When I use the functions rma() or justrma() in the Bioconductor affy package, the standard errors for the expression estimates computed by the function se.exprs() is a matrix of NA's. I am wondering if any of you have encountered this problem and if there is a solution. Any help would be appreciated. Thanks, Karthik. [[alternative HTML version deleted]]

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

Hi all, I tried to do normalization of affymetrix data with bioconductor on a Linux server. When I read in the cel files all seemed ok. But the next step caused an error. With Win XP all works fine. Did anyone experience similar problems? Thanks, Thomas > PI <- ReadAffy() > PI AffyBatch object size of arrays=712x712 features (14 kb) cdf=ATH1-121501 (??? affyids) number of

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

hi i have a huge matrix and want to split it into 2. with the command %%2. but i get this warning message: *"Error in mmat%%2 : non-numeric argument to binary operator*" here's the bit from my matrix: V1 V2 [1,] "Affymetrix:CompositeSequence:ATH1-121501:244901_at" "2.653" [2,]

venik wrote: > > I am trying in vain to find the bioDist package. > More generally, where can I find a lit of packages and their location? I > thought CRAN will have it, but I had no luck with bioDist. > Google bioDist, second hit (maybe another one, depending on your language settings). D -- View this message in context:

I''m trying to follow Chapter 10 of the howto and apply it to two ubuntu machines each with two 802.11b/g interfaces. However, I cannot get a connection. I would like the 4 interfaces to create 2 ad hoc links on separate channels. I have set this up successfully with the following: /etc/dbus-1/event.d/25NetworkManager stop wlanconfig ath0 destroy wlanconfig ath0 create wlandev wifi0

I am doing some testing of openwrt'd wireless access points, using madwifi-ng'd atheros radios. In the test configuration, I have three devices in a triangle, each has wds links to the other two devices. The ath0 interface is in ap mode, ath1 is a wds link to one device, and ath2 is a wds link to the other device. All three interfaces (and an ethernet interface) are in a bridge (br-lan)

Dear R-mailing list Hope you can help me. I am using R for windows to analyze my 107 HGU133Plus2.0 chips, however, R chrash when I try to use ReadAffy(). I want to buy a computer that can handle all these arrays, do you know how big a computer I need to buy? Best, Skov, Denmark [[alternative HTML version deleted]]

Recently ran into a problem with the 2.6.18 kernel on Xscale arch when a br= idge, with multiple interfaces on it, is configured with a redundant loop. = All interfaces are left on forwarding and nexer switch to block when the lo= op is introduced. This was tested against a 2.6.16 kernel and the problem d= id not occur, interfaces forwared and blocked correctly. Any help would be = appreciated.

Hi. I have problem in following scenario: 3 routers A, B, C: router A: eth0--> DSL ( public IP ) eth1 --> 192.168.0.1 ( local network ) routing table A: 83.x.x.x/29 dev eth0 proto kernel scope link src 83.x.x.x 192.168.5.0/24 via 192.168.0.8 dev eth1 192.168.4.0/24 via 192.168.0.8 dev eth1 192.168.3.0/24 via 192.168.0.8 dev eth1 192.168.2.0/24 via 192.168.0.8 dev eth1 192.168.1.0/24

Hi All, Type uniquing for C++ is in. Some data for Xalan with -flto -g: 9.9MB raw dwarf size, peak memory usage at 2.8GB The raw dwarf size was 58MB, memory usage was 7GB back in May, 2013. Other efforts at size reduction helped, and type uniquing improved on top of those. Data on building clang with "-flto -g" after type uniquing: 3.4GB MDNodes after parsing all bc files, 7GB

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 friends, i am sending this to centos mailinglist as i didnt solved problem and guys from madwifi are probably dead, as they are not giving me any reply . Thanks D. ---------- Forwarded message ---------- From: David Hl??ik <david at hlacik.eu> Date: Wed, Mar 19, 2008 at 11:39 AM Subject: ath_pci in modprobe.conf on Centos/Fedora To: madwifi-users at lists.sourceforge.net Hi friends,

I am trying to work with 75 affymetrix U133plus2 chips and am running into memory allocation errors when trying to merge or convert probe level data to expression values. I keep getting - Error: cannot allocate vector of size 561011 Kb and that is simply with a data subset. Is there a way around this limitation? -- Rodney A. Staggs Cancer Center Informatics Shared Resource 425 Delaware St S.E.

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The Bioconductor core group would like to announce the 1.3 release of the Bioconductor software. There are many new packages as well as several major upgrades and fixes in older packages, and users are encouraged to check them out. Release 1.3 is intended to be operated with R version 1.8.X, which can be obtained at CRAN (http://cran.r-project.org/) -- WHAT FEATURES DOES THIS RELEASE PROVIDE?

The Bioconductor core group would like to announce the 1.3 release of the Bioconductor software. There are many new packages as well as several major upgrades and fixes in older packages, and users are encouraged to check them out. Release 1.3 is intended to be operated with R version 1.8.X, which can be obtained at CRAN (http://cran.r-project.org/) -- WHAT FEATURES DOES THIS RELEASE PROVIDE?