similar to: problem in installing "simpleaffy"

Hi everybody, I have a problem when trying to do the quality control with the packages simpleaffy and affyQCReport with the drosophila chip 2.0 At first I got the messeage, that the *.qcdef file is not there. I followed the instructions in tha manual and created the file like that: array drosophila2cdf alpha1 0.05 alpha2 0.065 spk bioB AFFX-r2-Ec-bioB-3_at spk bioC AFFX-r2-Ec-bioC-3_at spk bioD

Hello, After running R CMD check on my package I received the following error on package dependencies: * using log directory 'C:/z-zBackup/Nuvera Bio on Iatros01/Development/RPackages/nvNormalize/nvNormalize.Rcheck' * using R version 2.9.1 (2009-06-26) * using session charset: ISO8859-1 * checking for file 'nvNormalize/DESCRIPTION' ... OK * checking extension type ... Package *

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 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

Hi, I decided to upgrade to 1.8 today... :-) Anyway, we are writing our own package that is dependent on a bioconductor library - 'affy'. I've checked and when I fire up R, library(affy) behaves as expected... so it all seems to be installed and OK... In the DESCRIPTION file in my package source I have the line: Depends: affy When I run R CMD check simpleaffy I get to: ... *

Hi again, I have been playing around with the order of loading packages, and as far as I can tell, there's nothing specific with affycoretools that's causing my Rgui to crash (i.e., shuts down and the Microsoft 'please send error report' box pops up). Instead, it has something to do with the order & type of packages that are loaded that add items to the menu bar by

Hallo, I just installed all needed packages for my project on my PC. But I cannot load all at one time. I now want to load limma. How can I realize the following plan: I want to install for example limma inclusive all needed other sub packages (add-on). Can anyone tell me the corresponding command? Thanks, Corinna Here is the result of the command library(): Pakete in Library

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I always followed http://cran.r-project.org/bin/linux/ubuntu/ to install R on Ubuntu 8.1. I had no errors before! > install.packages("XML") Warning in install.packages("XML") : argument 'lib' is missing: using '/usr/local/lib/R/site-library' --- Please select a CRAN mirror for use in this session --- Loading Tcl/Tk interface ... done trying URL

I am trying to use package ROCR to analyze classification accuracy, unfortunately there are some problems right at the beginning. Question 1) When I try to run demo I am getting the following error message > library(ROCR) > demo(ROCR) > if(dev.cur() <= 1) .... [TRUNCATED] Error in get(getOption("device")) : wrong first argument When I issue the command > dev.cur() it

Dear Sir/Madam, I could succesfully normalise my microarray data using marrayNorm package. However, i have not been able to get normalised red and green channel intensities through R package. Is there a possibility to write a formula to calculate back the red and green channel intensities after normalisation of the data. Do I need to incorporate this formula in my R script? I am biologist

I have recently upgraded to Ubuntu Gutsy and, for the first time, am using a 64-bit installation. After failing miserably to install R from source, not a problem for me in the past with a 32-bit install, I went the route of using the Debian Etch build. This went smoothly, but I am unable to update my numerous R and BioConductor packages, getting non-zero exit status errors on each package. Is

Dear sir/madam, I have been using R for a while now for microarray analysis, and I would like to make a "master" data frame in which I can combine information from many different sources. The basic list a genelist with 25.000 probes, then I would like to have a subcompartment with the statistical information, a subcompartment with more extensive information regarding each gene, and then

Dear Sir/Madam, I am doing a project related to R. However, it is always difficult find some R functions. The R user guide seems not complete. Is there any free document about all R functions ? Who knows ? please help me. My email is myzhaogong@yahoo.com Thank you very much --------------------------------- [[alternative HTML version deleted]]

Respected Sir/Madam, As I was developing some part of compiler for a project. I require grammar (BNF or EBNF) for converting the C code in the IR as it is not been mentioned any where over your official website. Awaiting for your help. Regards, Vijay Daultani. M.Tech student IIT Delhi

Respected sir/madam can you please suggest what is an unexpected symbol in the below code for running a multinomial logistic regression model <- multinom(adoption ~ age + education + HH size + landholding + Farmincome + nonfarmincome + creditaccesibility + LHI, data=newdata) [[alternative HTML version deleted]]

Dear Sir/Madam, I am using R version 1.8.1. I am doing following tast: First generate 100 Gaussion(3,1) numbers, then write the likelihood function to estimate the parameters of Gaussian distribution by direct maximizing the likelihood function. My likelihood function is: >fn<-function(x) >(-50*log((sd(x))^2))-50*log(sqrt(2*pi))-(1/2*((mean(x))^2))*(sum((x-(mean(x))^2)) After I

Dear Sir/Madam, I found your email address and your correspondence with R-users. I hope you could help me with this question about the function "ur.ers" in the package of "urca". It is an improved unit root test (Elliott et al. 1996 Econometrica). Do you know how to extract the value of the test statistic from the output? The only thing I can get is the print-out of all

Every now and then I get an alert like this one. I have no clue what this "rear" subsystem is, or why madam would be trying to write to its log file. Can anyone enlighten me? thanks in advance! ------------------------- SELinux is preventing /usr/sbin/mdadm from write access on the file /var/log/rear/rear-fcshome.log.lockless. ***** Plugin restorecon (93.9 confidence) suggests

Hallo sir/madam, I have a Chinese brand Ultrasound unit Ivis 60 model which had issues with booting after power fluctuations here in Congo -Africa. It is using a syslinux 3.31 which is continually giving problem when trying to enter BIOS so that I can install new files available on the usb disk. To enter bios you have to continually press "delete button" when starting the unit but no