search for: 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 bi...

Dear Madam/ Sir, I am using?R version 3.4.2.?I want to analyse microarray data. when I want to install "simpleaffy" package I get this error "package ?simpleaffy? is not available (for R version 3.4.2)". I have the same problem with?R version 3.3.2. Could you please help me to solve it? I am working with RStudio 0.99.903.exe. I also have problem in getting the new release of RStudio. Could you pl...

...rmalize/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'nvNormalize' version '1.0' * checking package name space information ... OK * checking package dependencies ... ERROR Namespace dependencies not required: affy affyio hgu133acdf hgu133plus2cdf simpleaffy See the information on DESCRIPTION files in the chapter 'Creating R packages' of the 'Writing R Extensions' manual. I've looked at the manual but cannot figure out if the problem is in the way I have specified dependencies in NAMESPACE or DESCRIPTION. It appears that dependec...

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 the cdfname file by using data<-ReadAffy(cdfname="hu6800cdf") but it still returns the same error. The version of R that...

...: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, simply type: openVignette() For details on reading vignettes, see the openVignette help page. Loading required package: reposTools Welcome to 'simpleaffy' V 2.1.3 Produced by The Paterson Institute for Cancer Research and funded by CANCER RESEARCH UK. http://bioinformatics.picr.man.ac.uk/simpleaffy mailto: microarray at picr.man.ac.uk Background...

...g 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: ... * checking package dependencies ... ERROR Packages required but not available: WARNING: ignoring environment value of R_HOME Prompt > Any ideas what is going on - as far as I can see the only dependency is to affy which is there and OK... I get no list of packages that are mis...

...he openVignette help page. > > >Loading required package: affyio >Loading required package: affydata >Loading required package: Biobase >Loading required package: gcrma >Loading required package: matchprobes >Loading required package: reposTools >Loading required package: simpleaffy >Loading required package: genefilter >Loading required package: survival >Loading required package: splines >Welcome to 'affyQCReport' V 1.6-1 >Further information available at: www.bifix.org > mailto: craig.parman at bifix.org >Loading required package: ade4 &g...

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...objects ROC utilities for ROC, with uarray focus rpart Recursive Partitioning RSQLite SQLite interface for R siggenes Multiple testing using SAM and Efron's empirical Bayes approaches simpleaffy Very simple high level analysis of Affymetrix data sma Statistical Microarray Analysis spatial Functions for Kriging and Point Pattern Analysis splines Regression Spline Functions and Cl...

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

...packages(pkgs = pkgs, repos = repos, dependencies = >> dependencies, ... : >> installation of package 'gcrma' had non-zero exit status >> 10: In install.packages(pkgs = pkgs, repos = repos, dependencies = >> dependencies, ... : >> installation of package 'simpleaffy' had non-zero exit status >> 11: In install.packages(pkgs = pkgs, repos = repos, dependencies = >> dependencies, ... : >> installation of package 'affyPLM' had non-zero exit status >> 12: In install.packages(pkgs = pkgs, repos = repos, dependencies = >> de...

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