search for: affybatches

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 f...

promptClass fails to identify methods associated with the class. Here is a fix: Index: promptClass.R =================================================================== --- promptClass.R (revision 41719) +++ promptClass.R (working copy) @@ -165,7 +165,7 @@ if (nmeths > 0) { .meths.body <- " \\describe{" for (i in 1:nmeths) { - .sigmat

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="") >

Running R2.4.0 on 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",

Hello Everyone, I am writing programs in R from 7 months and I am able to solve most of the errors/issues except for this current 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

dear all, I have a problem with a masked object in a package we created here. we make a package for a workflow of internal analysis of microarray data. to create the package we used: > install.packages(pkgs="affyAnalysis", repos=NULL) > R CMD INSTALL affyAnalysis Erzeuge Verzeichnisse ... Erzeuge DESCRIPTION ... Erzeuge NAMESPACE ... Erzeuge Read-and-delete-me ... Kopiere

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

...m able to combine the two S4 objects using merge function. > merge.fish <-merge(wild.fish,Dicer.fish) > merge.fish AffyBatch object size of arrays=712x712 features (17833 kb) cdf=Zebrafish (15617 affyids) number of samples=6 number of genes=15617 annotation=zebrafish notes=Merge from two AffyBatches with notes: 1) , and 2) > design Wild Mz_Dicer GSM95623.CEL 1 0 GSM95624.CEL 1 0 GSM95625.CEL 1 0 GSM95617.CEL 0 1 GSM95618.CEL 0 1 GSM95619.CEL 0 1 > fit <-lmFit(merge.fish, design) Error in as.vector(data) : n...

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

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 <-

Hi, I have built R (current development version) and BioConductor 1.7 with portland group compiler on a AMD Opteron. When I ran qc assessment on Affymetrix latin square data set, I got the following output, Loading required package: affy Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view,

Hi I'm running the latest R on a 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)

...cient than read.affybatch. Also, affy no longer depends on the affydata package. For this reason some examples have been moved from affy vignettes to the affydata vignette. The previously deprecated express function has been completely removed. Lastly, most normalization routines for AffyBatches can now be called with the parameter type which specifies whether the normalization should be applied as a PM-only, MM-only, both PM and MM together or PM and MM separately. --- affycomp: New assessment was added: assessSpikeIn2. Examples of new feature: Local slopes are computes...

...cient than read.affybatch. Also, affy no longer depends on the affydata package. For this reason some examples have been moved from affy vignettes to the affydata vignette. The previously deprecated express function has been completely removed. Lastly, most normalization routines for AffyBatches can now be called with the parameter type which specifies whether the normalization should be applied as a PM-only, MM-only, both PM and MM together or PM and MM separately. --- affycomp: New assessment was added: assessSpikeIn2. Examples of new feature: Local slopes are computes...

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

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 HTML version deleted]]

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 case but would like

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

To whom it may concern, I am a student from 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.