search for: dnacopy

Hi All: Has anyone analyzed Illumina 550K data using DNAcopy package? I have around 2300 samples. According to Venkatraman and Olshen 2007 paper, it needs about 25 min to run a single sample for Affymetrix 100K. I am afraid it will take too long to analyzed my data. Anybody has an idea? Thanks! Best, -- View this message in context: http://www.nabble.com/...

Hello R Developers I am using DNACopy package http://bioconductor.org/packages/1.9/bioc/html/DNAcopy.html I am not able to figure out how to (if at all possible) to modify output format, namely, I am getting the following: "ID" "chrom" "loc.start" "loc.end" "num.mark" "seg.mean&qu...

Hi All, I am using DNAcopy package in R for copy number analysis of 500K chip. The final output which I get from DNA copy is too big to be printed in a file. So I am getting an error as "reached getOption("max.print") -- omitted 475569 rows " Can somebody please provide me the pointers with how to inc...

...for example). Then in an Rd file, we have if (require(strucchange)) { # Doing some examples making use of strucchange } The CRAN check results reports the following NOTE: checking for unstated dependencies in examples ... NOTE 'library' or 'require' calls not declared from: DNAcopy coda strucchange I note the same problems in other packages (e1071, Deducer, diveMOVE, gplots, ...) Any hints? I'm pretty confident that Suggests: is preferable to Depends: in such a case, but I can't seem to address this note. Thanks, Jay -- John W. Emerson (Jay) Associate Professor...

I am trying to build a package (GWASTools, submitted to Bioconductor) that uses the "sandwich" package. I have references to "sandwich" in DESCRIPTION: Imports: methods, DBI, RSQLite, sandwich, survival, DNAcopy and NAMESPACE: import(sandwich) In the code itself is a call to vcovHC: Vhat <- vcovHC(mod, type="HC0") I have sandwich version 2.2-7 installed. When I run R CMD check on my package, I get the following error during checking of examples: * using R Under development (unstable) (201...

...Aparna) > 70. My surprising experience in trying out REvolution's R (Jason Liao) > 71. Blanchard Quah/Impulse Response Functions (Laura Carvalho) > 72. fitting assimptotic decaing with - and + on X (milton ruser) > 73. Polyspline Integration (Denney, William S.) > 74. DNAcopy package in R (Selena Niu) > 75. Re: Fitting linear models (Dimitri Liakhovitski) > 76. Re: Fitting linear models (Marc Schwartz) > 77. Re: Fitting linear models (Vemuri, Aparna) > 78. Re: bug when subtracting decimals? (hadley wickham) > 79. Re: Fitting linear models (Dimit...

...=== All packages from the 1.3 release are included. All current bug fixes have been applied, and most have upgraded and provide enhanced functionality. SOME OF THE MAJOR UPGRADES FOR RELEASE 1.4: =========================================== -- Proteomics (PROcess, gpls, apComplex) -- Array CGH (DNAcopy, aCGH) -- Cell cycle analysis (GeneTS) -- 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) -- affymet...

...te: Tue, 31 Mar 2009 14:47:52 +0530 From: "pooja arora" <pooja_arora@persistent.co.in> Subject: [R] how to increase the limit for max.print in R To: <r-help@r-project.org> Message-ID: <003d01c9b1e1$91dce2a0$b596a7e0$@co.in> Content-Type: text/plain Hi All, I am using DNAcopy package in R for copy number analysis of 500K chip. The final output which I get from DNA copy is too big to be printed in a file. So I am getting an error as "reached getOption("max.print") -- omitted 475569 rows " Can somebody please provide me the pointers with how to inc...