search for: affybatch

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...

...trato <cstrato at aon.at> writes: > >> Dear all, >> >> What is the best way to write the docs for S4 classes? >> >> Concretely, is it possible to include the methods in the class >> documentation? >> For example, the documentation for class "AffyBatch" contains all methods. >> However, when I do: >> promptClass("AffyBatch") >> the relevant output of file "AffyBatch-class.Rd" is: >> \section{Methods}{ >> No methods defined with class "AffyBatch" in the signature. >>...

Hi! Is There a way to manually create an affybatch object from qPCR array data? -- View this message in context: http://r.789695.n4.nabble.com/Creating-affybatch-objects-from-matrix-data-from-qPCR-array-tp3921559p3921559.html Sent from the R help mailing list archive at Nabble.com.

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="") >

...Apple Mac OS X 10.4.8, in Emacs ESS mode, and also R.app. In an attempt to learn a bit more about a particular method (geneNames in package affy) I invoked getMethods("geneNames") which produced geneNames methods, but not the one in affy (output below). I had to know the signature (AffyBatch) in order to find the method > getMethod("geneNames", "AffyBatch") Isn't getMethods() supposed to get them all? Is this a problem, or bug, or am I misunderstanding something? I try to use getMethods() to learn how things work, without having to always get the source...

...urrent post. My Task is to read a Microsoft Excel file(textE_to_affy.csv) which contains the Microarray Expression Values collected from the Illumina Microarray experiment. These collected intensity values need to be normalized(Rank Invariant Normalization) by using the R function "normalize.AffyBatch.invariantset()". Since the normalize.AffyBatch.invariantset() method requires the input argument to be an AffyBatch Object, I used the read.exprSet() method to convert the intensity values present in the (textE_to_affy.csv) file into an AffyBatch Object as follows: > testFile <- temp...

...et: preprocessCore Attache Paket: 'affyPLM' The following object(s) are masked from package:affyAnalysis : preprocess The following object(s) are masked from package:stats : resid, residuals, weights The preprocess command in the affyPLM package needs an affybatch object to work with. our preprocess is as such definiert: preprocess <- function(x,...) UseMethod("preprocessExpData") preprocessExpData.expData <- function(data){ require("vsn") data <- list(ExpressionSet=vsnrma(data$AffyBatch), baseDir=data$baseDir,experiment...

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 two data set of normalized Affymetrix CEL files, wild type vs Control type.(each set have further three replicates). > wild.fish AffyBatch object size of arrays=712x712 features (10 kb) cdf=Zebrafish (15617 affyids) number of samples=3 number of genes=15617 annotation=zebrafish notes= > Dicer.fish AffyBatch object size of arrays=712x712 features (10 kb) cdf=Zebrafish (15617 affyids) number of samples=3 number of genes=15617 annotat...

Hi all, I tried to do normalization of affymetrix data with bioconductor on a Linux server. When I read in the cel files all seemed ok. But the next step caused an error. With Win XP all works fine. Did anyone experience similar problems? Thanks, Thomas > PI <- ReadAffy() > PI AffyBatch object size of arrays=712x712 features (14 kb) cdf=ATH1-121501 (??? affyids) number of samples=6 number of genes=506944 annotation=ath1121501 notes= Warning messages: 1: Line starting '<TITLE>Error</TITLE> ...' is malformed! 2: Line starting '<BODY> ...' is malfor...

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 <- expresso(affyBatch,bgcorrect.method="rma",normalize.method="quantiles",summary.method="medianpolish") background correction: rma normalization: quantiles PM/MM correction : expression values: medianpolish back...

...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 correcting Retrieving data from AffyBatch...done. Computing expression calls... .........................done. scaling to a TGT of 100 ... Scale factor for: 0203_YH10_H_MCF7_r1.CEL 0.291660289301555 Scale factor for: 0203_YH11_H_MCF10A_r1.CEL 0.42025300545212 Scale factor for: 0203_YH12_H_a100MCF7_r1.CEL 0.287589038746987 Scale factor for:...

...presumably up to date Linux server. 'Doing something silly I'm sure, but can't see why my saved PLMset objects come out all wrong. To use an example: Setting up an example PLMset (I have the same problem no matter what example I use) > library(affyPLM) > data(Dilution) # affybatch object > Dilution = updateObject(Dilution) > options(width=36) > expr <- fitPLM(Dilution) This works, and I'm able to get the probeset coefficients with coefs(expr). until I save and try reloading: > save(expr, file="expr.RData") > rm(expr) # just to be s...

...enhanced functionality. -- NEW PACKAGES AND MAJOR UPGRADES FOR RELEASE 1.3 -- The following is an overview of the most important changes, additions, and upgrades: --- affy There have been many improvements to the affy package. There were big speed and memory improvement of ReadAffy, read.affybatch, justRMA. A mas5calls method was added to get Affymetrix's P/M/A calls. Cel and Cdf classes are no longer supported. Function, read.celfile and other Cel related methods and functions removed. Most Cdf related functions have moved to the makecdfenv package. Function read.probe...

...enhanced functionality. -- NEW PACKAGES AND MAJOR UPGRADES FOR RELEASE 1.3 -- The following is an overview of the most important changes, additions, and upgrades: --- affy There have been many improvements to the affy package. There were big speed and memory improvement of ReadAffy, read.affybatch, justRMA. A mas5calls method was added to get Affymetrix's P/M/A calls. Cel and Cdf classes are no longer supported. Function, read.celfile and other Cel related methods and functions removed. Most Cdf related functions have moved to the makecdfenv package. Function read.probe...

On Sat, Feb 14, 2009 at 00:17, <ashrafi@ucdavis.edu> wrote: Hi, I was trying to read ~400 chips in an affybatch and I got the same message. Could you find a remedy for that. My server has 128 GB of RAM. However, R halted ever before it uses the memory. I have been able to load upto 250 CEL files but this time I wanted to test what would happen if I want to normalize 400 chips. Thanks for your prompt res...

Dear R/Biocondutor users: I tried to merge two big affybatch data sets in R (under unix mainframe) and encounter the problems as following: combine2.3<-merge(combine2.1,TALL) Error: cannot allocate vector of size 409600 Kb I do not know what is the problem and how can i fix the problem. any suggustion will be appreciated. liping [[alternative HTM...

I am trying to preprocess a large dataset of affymetrix data. Creating an affybatch is not possible with the computer I am running it on, so I have used the justRMA command to run RMA. I have read the affy document describing the justRMA command and the help documentation but I am unclear as to whether this command uses median polish after normalization. I assume this is the cas...

Dear all, I am currently analyzing a set of arrays hybe on the lattest affy Drosophila 2.0 GeneChip. I am trying to run simple annaffy analysis but can¹t find what is the name of the annotation file I need to use. Here is the output of the AffyBatch object I am using: > expData AffyBatch object size of arrays=732x732 features (16749 kb) cdf=Drosophila_2 (18952 affyids) number of samples=4 number of genes=18952 annotation=drosophila2 So when I try to use and annaffy procedure I get: >Symbol = aafSymbol(geneIDs, "drosophila2")...

...rom Peking University, China. I am currently doing some microarray data analysis research with Bioconductor package of R. Problem arises when I try to import into R my dataset which contains 109 samples (total size more than 1.4 GB). The memory limit of R makes importing all the samples into one AffyBatch object a "mission impossible" for me. Though it will be possible to import data into several AffyBatch objects, and do the preprocessing respectively. Yet in this case, the results of background correction or normalization are not desirable, because not all the information known (namel...