search for: affypdnn

Dear all, I am a PhD student working with Affymetrix HGU133atag array for analyzing the Latin square experiment. I was trying to generate gene expression index for hgu133atag array for PDNN model. While extracting the chiptype specific data structure, I got the following error- > library(affypdnn) Loading required package: affy Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. registerin...

...ws Server 2008 R2 Enterprise for the 64-bit builds, and R-2.12 (2010-08-26 r52817) on both machines: >>> On 64-bit Windows: R\bin\R.exe CMD build ACME --> produces no output at all and returns code 0. >>> On 32-bit Windows: R\bin\R.exe CMD check --no-vignettes --timings affypdnn_1.23.0.tar.gz * using log directory 'E:/biocbld/bbs-2.7-bioc/meat/affypdnn.Rcheck' * using R version 2.12.0 Under development (unstable) (2010-08-26 r52817) * using platform: i386-pc-mingw32 (32-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for f...

...- Packages for lab assay analysis and management (prada) -- Agilent arrays handling in limma -- Annotation tools (Resourcer, GOstat, goTools, ontoTools) -- Improved interfaces (limmaGUI, affylmGUI, webbioc, -- MAGE file processing (RMAGEML) -- affymetrix processing: many improvements, gcrma, affypdnn (probe-dependent nearest neighbors), affyPLM (probe-level models). -- marray (next generation of the depreciated marrayClasses, marrayNorm, marrayPlots, marrayTools packages) -- General analysis tools (rama, qvalue, pickgene, EBarrays, impute, pamr, bim, ) -- QA/QC (arrayMagic, arrayQu...

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