similar to: Problems with expresso

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

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, 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

Hi!I'm doing a little data importing from .cel files, > setwd("/home/mandova/celfiles") > mydata<-ReadAffy() Error in sub("^/?([^/]*/)*", "", filenames, extended = TRUE) : unused argument(s) (extended = TRUE) Then I tried > filenames<-paste("GSM",c(seq(138597,138617,1)),".cel",sep="") >

hi all, Am new to R. I am having problems installing Bioconductor package in R on fedora core 4 running on AMD64 bit machine. this is the error message I get : gcc -shared -L/usr/local/lib -o affyPLM.so avg_log.o biweight.o chipbackground.o common_types.o do_PLMrlm.o do_PLMrma.o do_PLMthreestep.o idealmismatch.o LESN.o lm.o lm_threestep.o log_avg.o matrix_functions.o

Hi, I'm working with custom slides(Cy5) and working in the normalization of the arrays. I have three arrays (technical replicates). I have sucesfully normalized the data using vsn, however i would like to normalize using spike in controls. My controls are annotated as CTL-1 to x and i would like to do etiher a normalization by block per array or the mean of all the controls per array. The gal

Hi there, I got a problem when trying to read in a .cel file using ReadAffy(). R codes: require(affy) ReadAffy(filenames="CH1.CEL") It failed and I got the error, Error in read.celfile.header(as.character(filenames[[1]])) : Is CH1.CEL really a CEL file? tried reading as text, gzipped text, binary, gzipped binary, command console and gzipped command console formats Also, I tried

Hi, I am wondering how to make a function Fun to make the following work: t0 <- (paste("hgu133a", "ENTREZID", sep="")) xx <- as.list(Fun(t0)) # make it work like xx<-as.list(hgu133aENTREZID) thanks, -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed..." ---Matrix III

Hello, Im trying to combine 3 affybatches (1x hgu133+2 array and 2x hgu133a array) Im useing this script: library(matchprobes) library(affy) library(AnnotationDbi) library(hgu133plus2probe) library(hgu133aprobe) library(hgu133a.db) u133p2 = ReadAffy() # reading hgu133 +2 cel file into affybatch u133a1 = ReadAffy() # reading hgu133a cel file into affybatch u133a2 = ReadAffy() # reading hgu133a

The Bioconductor core group would like to announce the 1.3 release of the Bioconductor software. There are many new packages as well as several major upgrades and fixes in older packages, and users are encouraged to check them out. Release 1.3 is intended to be operated with R version 1.8.X, which can be obtained at CRAN (http://cran.r-project.org/) -- WHAT FEATURES DOES THIS RELEASE PROVIDE?

The Bioconductor core group would like to announce the 1.3 release of the Bioconductor software. There are many new packages as well as several major upgrades and fixes in older packages, and users are encouraged to check them out. Release 1.3 is intended to be operated with R version 1.8.X, which can be obtained at CRAN (http://cran.r-project.org/) -- WHAT FEATURES DOES THIS RELEASE PROVIDE?

Hi, I got an interesting programming challenge: How do you inspect an object which is assigned via delayedAssign() and that throws an error as soon as it is "touched" (=the value is evaluated)? Is it possible? MINIMAL EXAMPLE: $ R --vanilla > delayedAssign("foo", stop("Hey!")) (If you find this minimal example silly/obvious, please skip down to the real

On Mon, Jan 26, 2015 at 12:24 PM, Hadley Wickham <h.wickham at gmail.com> wrote: > If it was any other environment than the global, you could use substitute: > > e <- new.env() > delayedAssign("foo", stop("Hey!"), assign.env = e) > substitute(foo, e) > > delayedAssign("foo", stop("Hey!")) > substitute(foo) Hmm... interesting

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 all , I have one query. i have list of some .cel files. in my program i have to mention the path of these .cel files part of my program is, rna.data<-exprs(justRMA(filenames=file.names, celfile.path=*datadir*, sampleNames=sample.names, phenoData=pheno.data, cdfname=cleancdfname(hg18_Affymetrix U133A))) in the place of "datadir" i have to mention the character string of the

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)

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,

If it was any other environment than the global, you could use substitute: e <- new.env() delayedAssign("foo", stop("Hey!"), assign.env = e) substitute(foo, e) delayedAssign("foo", stop("Hey!")) substitute(foo) Hadley On Mon, Jan 26, 2015 at 12:53 PM, Henrik Bengtsson <hb at biostat.ucsf.edu> wrote: > Hi, I got an interesting programming

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

Hello, I'm very new in working with tcl/tk in R and have a problem which will probably sound silly to most of you. Here is the code I have problems with: readcelfiles <- function() { require(tcltk) tt <- tktoplevel() tkgrid(tklabel(tt,text="Choose a directory!")) OnOK <- function() { fileDir<-tclvalue(tkchooseDirectory()) data.raw <-