similar to: File in use error (PR#4047)

Dear R Users, In the expresso function, which combination of these methods for data pre-processing (when using affymetrix oligo arrays) is the best: bgcorrect.metod = rma rma2 mas normalize.method = qspline quantiles loess pmcorrect.method = pmonly subtractmm mas summary.method = liwong avgdiff medianpolish mas There are many options within each method. I would appreciate a hint on the best

Full_Name: Eric Libby Version: 2.1.1 OS: OS Tiger Submission from: (NULL) (65.93.158.117) I am trying to analyze microarray data of 42 human arrays. I typed in the following instructions: library(affy) Data <-ReadAffy() eset <- expresso(Data, normalize.method="invariantset", bg.correct=FALSE, pmcorrect.method="pmonly",summary.method="liwong") And I get some

Hi, I have a question concerning the analysis of some affymetrix chips. I downloaded some of the data from GEO GSE11324 (see below). In doing so I'm stuck after I identified the probesets with significant changes. I have problems in assigning probeset specific gene names as well as getting the genomic coordinates. Furthermore I have no clue how to deal with the fact, that most genes have

Hello, I want to use expresso for preprocessing the hgu133a-spikein data from affycompII. But there is an error: > library(affy) > path <- "z:/Microarray/hgu133a-spikein/rawdata" > celFile <- list.celfiles(path=path,full.names=TRUE); > affyBatch <- ReadAffy(filenames=celFile[1:6]); > eset1 <-

Happy new year to all; A few days ago, I posted similar problem. At that time, I found out that our R program had been 32-bit compiled, not 64-bit compiled. So the R program has been re-installed in 64-bit and run the same job, reading in 150 Affymetrix U133A v2 CEL files and perform dChip processing. However, the memory problem happened again. Since the amount of physical memory is 64GB, I think

Hi, all; I know there has been a lot of discussions on memory usage in R. However, I have some odd situation here. Basically, I have a rare opportunity to run R in a system with 64GB memory without any limit on memory usage for any person or process. However, I encountered the memory problem error message like this: Error: cannot allocate vector of size 594075 Kb I got this error message while

Resolve in the guest the given path, so absolute symlinks can be listed using appliance tools without resolution errors. Also remove the note about the possibility to escape the sysroot using ll and llz, since realpath won't return paths outside sysroot. Fixes part of RHBZ#1293276. --- daemon/ls.c | 28 ++++++++++++++++++++-------- 1 file changed, 20 insertions(+), 8 deletions(-) diff --git

I got a table on SQL Server, which has columns EquationId (int) and Formula (varch(900)). I need to select Formula with certain EquationId, for example, Select Formula from OGA_DEV.dbo.Equation where EquationId = 3 I tried to work within RGui using RODBC: > library(RODBC) > conn = odbcConnect("SQL Server") > odbcQuery(conn, "Select Formula from OGA_DEV.dbo.Equation where

Dear list members, When I modify the MFC sample (using the statconnector graphics device) to show a lattice graph in the Active X control (actually the wireframe from http://addictedtor.free.fr/graphiques/graphcode.php?graph=40 ) the program runs without generating any errors, but the data-driven part of the plot does not display. The bounding box is displayed, but not the axes or data within

HI: Is it possible to use the RODBC package within MS Access. I have been using from R but was just wondering if it could be used along with R(D)COM. Something like this: Dim dbs As DAO.Database Dim rst As DAO.Recordset Dim myApp As StatConnector Set myApp = New StatConnector myApp.GetErrorText myApp.Init "R" myApp.EvaluateNoReturn "library(RODBC)" myApp.EvaluateNoReturn

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

Hello, I am a newbie in R project and trying to call prcomp(x) of R function using (D)COM server communicate with R in ASP, and encountering the error "Runtime error -2147221493(8004000b). Automation Error, Object is static, operation not allowed." at line Result=StatConn.Evaluate("y<-prcomp(x)"). E ven I have added the line StatConn.EvaluateNoReturn("library

per IRC discussion, >From a1d982bf49e166341096902fc4c103d4397ce0e3 Mon Sep 17 00:00:00 2001 From: Jim Meyering <meyering at redhat.com> Date: Tue, 11 Aug 2009 13:16:27 +0200 Subject: [PATCH libguestfs] daemon/ls: make do_ll require root, like all the rest * ls.c (do_ll): Do invoke "NEED_ROOT" here, and add a FIXME to provide a "debug ll" command with the semantics

Hi. I can''t seem to get debugging of specs working in Netbeans. AFAIK, I''m supposed to be able to just do Command+Shift+F5 with the spec open in the editor but i get this error: /Users/admin/src/expresso/vendor/plugins/rspec/lib/spec/test/unit/autorunner.rb:2:in `remove_method'': method `process_args'' not defined in Test::Unit::AutoRunner (NameError)

Hello, I'm trying to make a function for using wine_get_unix_file_name in VB6 programs. Private Declare Function lstrcpyA Lib "kernel32.dll" (ByVal lpString1 As String, ByVal lpString2 As Long) As Long Public Declare Function GetProcessHeap Lib "kernel32" () As Long Public Declare Function HeapFree Lib "kernel32" (ByVal hHeap As Long, ByVal dwFlags As

Hi. My VB program run a R - script located in the server with R DCOM server. The R - script is designed to send a query to DB through ODBC. There is NOT any problem when I run each code from R-window interface. However, when I call the R-script from my VB program it stucked after calling "sqlQuery" statement. I can check that odbcConnect(dsn, uid, pwd) returns -1.

Hi All, I have microarray data that does not come in a CEL file. Currently it is in the form of columns = individual samples and rows = individual probes. There are about 79 columns and it is in a tab delimited text file. Is there a way to convert this file into an AffyBatch so that I can run expresso with it? Thanks, George

Hi All, I am using the R ActiveX component (v1.2). I have written a custom function in R which returns a dataframe. I want to be able to retrieve the contents of the returned dataframe in my application. Here is a snippet of the code (line that throws exception). X has been correctly declared and init'ed earlier on in the code. x.EvaluateNoReturn("results_frame <-

I have been trying to write a "proper" print method for a package, and have almost gotten what I want. From a reading of the relevant section in R Extensions and the introduction to methods, I've stuck the whole business into a character object and used: NextMethod("print") However, instead of not printing quotes and displaying the usual representation of the string,

Hi, all-- I wanted to start a (new) thread on R speed/benchmarking. There is a nice R benchmarking overview at http://www.sciviews.org/other/benchmark.htm, along with a free script so you can see how your machine stacks up. Looks like R is substantially faster than S-plus. My problem is this: with 512Mb and an overclocked AMD Athlon XP 1800+, running at 588 SPEC-FP 2000, it still takes me