similar to: Memory allocation

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 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

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. 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

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.

How can I get a single backslash in a character string? My goal is to escape dots in a string that will be used as a regular expression. I thought I could do it this way: gsub(".", "\\.", x) Unfortunately, "\\" does not represent a literal backslash as I expected, but rather a pair of backslashes: > "\\." [1] "\\." > "\\" [1]

Hi, I have been able to successfully install Samba4 and OpenLDAP and connect them via SSL. The file samba.schema is also loaded into OpenLDAP, but when I start samba server it looks like it is expecting some basic structure. My Question at this point is how to provide this the easisest way? Currently the OpenLDAP DB is entirely empty (virgin) so Samba4 could create anything it needs. cat

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]]

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]]

Hi all, I have a client that has 4 subnets within his building, internet, office, business center and wireless. My plan is to use Shorewall but I have never tested it with more than 2 interfaces. Is this possible? Would there be any issues that might arise. Each subnet would have access to the internet but there will be no communications allowed between the others. Thanks in advance....

I just implemented a system using a TE411P hardware echo cancellation card. Per Digium, I setup zaptel.conf, and zapata.conf the same way as I always have. To my surprise calls out to the PSTN had a terrible echo. 1 - 2 second delay, and quite clear. The echo was so bad that I had to remove the hardware echo cancellation module from the card. We are only using the 1st span of this card right

Hello! I use Debian GNU/Linux at work and I really like apt-get tool. As far as I understand the whole picture, there are now some Debian packages of R packages. Build of Debian packages is done automagically by Perl script. By the way, what is the status of Debianizing R packages? Is it stopped, just holded, ... I don't know so I am asking There is also Bioconductor and I am aware that the

Hi, I am running R 2.0.1.1. on Windows. It is a Dell Dimension with a 3.2 Ghz Processor and 4Gb RAM. When using the ReadAffy() function to read in 97 arrays, I get the below error messages: Error: cannot allocate vector of size 393529 Reached total allocation of 1024Mb: see help(memory.size) When I use the comman "memory.limit(size=4000)" to increase the memory size to the

I have two samba DCs (4.0.9) and no Windows DCs, and group policy is failing. I've narrowed it down to an error accessing the sysvol folder. Some clients (not all clients) get the error "Element not found" when connecting to our sysvol folder which is "\\ahc.pdc\sysvol\". The problem seems to be intermittent, a client may suddenly start working again, or suddenly stop.

I've finally been able to capture the panic, as now it occurs even with DDB configured. Of the six machines I have running 6.1-RC (CVSupped today), this is the only one that does this. /boot/kernel/kernel text=0x30c488 data=0x3b6a0+0x3170c syms=[0x4+0x46430+0x4+0x58da4] no such file or directory - Hit [Enter] to boot immediately, or any other key for command prompt. Booting

On Thu, 5 Jun 2003, Shaun Jurrens wrote: > On Wed, Jun 04, 2003 at 06:32:46PM +0200, Palle Girgensohn wrote: > #> Hi Shaun, > #> > #> Thanks for the input! Glad to hear I'm not the only one > #> > #> In my case, both the SCSI and NIC are integrated on the motherboard, so I > #> cannot really move them around... :) > #> > #> Also, as I

Hi all, I've stumbled upon some memory limitations for the analysis that I want to run. I've a matrix of distances between 38000 objects. These distances were calculated outside of R. I want to cluster these objects. For smaller sets (egn=100) this is how I proceed: A<-matrix(scan(file, n=100*100),100,100, byrow=TRUE) ad<-as.dist(A)

I'm trying to make a factor with levels for day of week, appear as Monday-Sunday, rather than alphabetically. I'm using reorder.factor from gdata package, but obviously not using it properly. What am I doing wrong? Thanks. >data <- read.table("DataEarly2008.txt", sep=" ", header=T, as.is=1:2) >str(data) 'data.frame': 7953 obs. of 9 variables: $

I'm hearing an echo when using a headset with my IP 501 / 601. The phones are using BR 3.1.2 and SIP 1.6.3. I use tftp to configure the phones. The sip.cfg is the default from polycom except for the parameters required to connect the phones to asterisk. I have absolutly no echo with the handset, but do have a slight echo on the speaker phone. I haven't ruled out room acoustics as the

Hey everyone, I've been doing a lot of research into a decent server for Asterisk but I seem to be running and circles and now I am turning to you. The issue I have is it needs to be rack mountable (so a Dell SC430 isn't going to work) and preferably have 3 pci ports. The problem that I seem to be running into is that when I look at servers from Dell or IBM or the like they only seem to