similar to: Help regarding mas5 normalization

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

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. >

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,

So the help for loadURL says: 'loadURL' is a convenience wrapper which downloads a file, loads it and deletes the downloaded copy. Trying to load an rda file on Windows (XP, R-devel) I was surprised when I received an error about input being corrupted with LF replaced by CR. The fix was to specify mode="wb" to loadURL. This gets passed to download.file and the right

Dear list, I am trying to prepare a handout showing how to use R for factor analysis. As part of the exercise I want to save a correlation matrix on a tutorial web page. I can save with no problem (saving locally and then transferring to the web site). Although I can load() the local file, I am having problems getting loadURL to read the remote file. I have tried saving it as an ascii

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 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!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="") >

I sent this on Friday but somehow managed to email it to the wrong email address! ---- Attached is a patch to add external (AJAX) loading of content to the InPlaceEditor. 2 extra options have been added: loadUrl: a URL to load the content from. If this is present, it will be used instead of the innerHTML. fieldId: I had to add this so we know what the text field is when we''ve

I realize that others have struggled with this issue...i.e. http://tolstoy.newcastle.edu.au/~rking/R/help/05/01/9826.html i am on os.x 10.4 w/ R2.2, and am (perhaps foolishly) also on this quest... i would like to be able to install downloaded source (tar.gz'd) files from within an R session, and have it work in a X-platform way..i am often not connected to the internet and have libraries

On 07/05/2015 09:17 AM, linush at verizon.net wrote: > Someone please tell me what I did to screw this thing up so badly. On 07/05/15, Gordon Messmer<gordon.messmer at gmail.com> wrote: Have you looked at the log files in /mnt/sysimage/root/? ------------- Quoting broken in this mailer ------------ So I looked in /mnt/sysimage/var/log/anaconda and found this in anaconda.packaging.log:

I have been installing CentOS for years using PXE, kickstart and NFS, but the procedure fails with CentOS 6.6 for some reason. A PXE-initiated, manual install goes through all the setup steps, and once rpm installation has started, it dies after a few packages: anaconda 13.21.229 exception report Traceback (most recent call first): File "/usr/lib/anaconda/yuminstall.py", line 1006,

Dear useR, Just wandering whether it is possible that there is any function in R could let me get the text contents for a certain website. Thanks a lot! Best, Leon [[alternative HTML version deleted]]

(Sorry for the slightly off topic post) I'm giving a talk (on data mining) to some non-statisticians (who're all postgrad students, but a mixture of Science and Commerce majors). My intention is to show them the importance of statistics when doing data mining. What I'm thinking of doing is using, hopefully, two datasets. One from scientific area and another that is

Hello I'm stuck with some notebooks having MacOS 10.2.8. After trying R-2.2.0 (which won't run), I had to settle with R 1.7.1, which runs fine. The problem is this: I have a csv file in a web server, which I'd wish to be able to load with d <- read.csv("http://server/path/cuestionario.csv") Unfortunately it doesn't work in R 1.7.1 / Mac, although the help page

a) I do not run gnome. I will *NEVER* voluntarily run gnome. I don't even want it installed. b) Click on link in an email in t-bird, and get this in the error console: Error: uncaught exception: [Exception... "Component returned failure code: 0x80004005 (NS_ERROR_FAILURE) [nsIExternalProtocolService.loadUrl]" nsresult: "0x80004005 (NS_ERROR_FAILURE)" location:

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

I just yum-installed the 2.6.9-34 kernel RPMs and rebooted, and lo and behold, my other onboard NIC is now detected, after a fashion. /etc/sysconfig/hwconf now has entries for: device: eth0 driver: forcedeth desc: "nVidia Corporation CK804 Ethernet Controller" device: eth2 driver: sky2 desc: "Marvell Technology Group Ltd. 88E8053 Gigabit Ethernet Controller" The device/desc

Hi, I am having difficulties accessing parent properties/attributes from the child. Anyone could shed some lights onto this? Heres a sample code: class Parent < ActiveRecord::Base :has_many => :childs @connector def before_save @connector = ''some connector object'' 0..9.do |count| self.childs << Child.new self.childs[count].connector =

Hello useRs, I'm trying to install bioconductor on ubuntu edgy eft and R 2.4.0. I have some error messages during installation, in particular for the package "affy" : "Error: package 'affy' required by 'makecdfenv' could not be found" I have tryed to install 'makecdfenv' with the command : getBioC("makecdfenv") But I have this message