similar to: encountering difficulty asking R to manipulate the correct columns in Expression Set class (object 4). (PR#13464)

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 R-helpers & bioconductor Sorry for cross-posting, this concerns R-programming stuff applied on Bioconductor context. Also sorry for this long message, I try to be complete in my request. I am trying to write a subset method for a specific class (ExpressionSet from Bioconductor) allowing selection more flexible than "[" method . The schema I am thinking for is the following:

Hi, I am having troubles with creating an eSet and would appreciate any help on the following problem. I am trying to create an eSet using the following code pd <- read.table(file="pdata.txt",header =TRUE,row.names=1); colnames(pd) <- c("type","tumor","time","id"); pdN <- list(type =

Hi, Can anyone help me of the affylmGUI package, I can't get it work and searched for google but can't find any proper solutions. I get the error information each time when I load my cells files, which are shown in the following links. ------------- http://clarezoe.googlepages.com/1.png http://clarezoe.googlepages.com/2.png http://clarezoe.googlepages.com/3.png ------------- Errors also

Hi all, What are current methods people use in R to identify mis-spelled column names when selecting columns from a data frame? Alice Johnson recently tackled this issue (see [BioC] posting below). Due to a mis-spelled column name ("FileName" instead of "Filename") which produced no warning, Alice spent a fair amount of time tracking down this bug. With my fumbling fingers

Hi all, I have this microarray large microarray data set (ALL) from which I would like to subset or extract a set of data based on a factor ($mol.biol). I looked up some example of subsetting in, picked up two commands and tried both but I got error messages as follows > testset <- subset(ALL, ALL$mol.biol %in% c("BCR/ABL","ALL1/AF4")) >> Error in

Hi, Reading help("Documentation"), I'm led to believe that a help call like: ?myFun(x, sqrt(wt)) Will search for help on the appropriate method in the case that myFun is generic. This isn't working for me. Here is an example using the Biobase package: ## If Biobase is not installed source("http://bioconductor.org/biocLite.R") biocLite("Biobase")

Hello, I am to run this R script but i keep getting this error. > expr<-exprs(golubMerge) Warning message: The exprSet class is deprecated, use ExpressionSet instead I tried to find information on the website but no luck. (exprSet...etc) thank you. -- View this message in context: http://www.nabble.com/expression-matrix-tp15912874p15912874.html Sent from the R help mailing list archive

On 10/11/2006 2:48 PM, Seth Falcon wrote: > Hi, > > Reading help("Documentation"), I'm led to believe that a help call > like: > > ?myFun(x, sqrt(wt)) > > Will search for help on the appropriate method in the case that myFun > is generic. This isn't working for me. Here is an example using the > Biobase package: > > ## If Biobase is

Hi, I'm very confused about R structures and the methods to go with them. I'm using R for microarray analysis with Bioconductors. Suppose without reading the documentations, what's the best way to explore a data structure when you know nothing about it? I am currently using is() / class() to see what the object is. str() / attributes() to probe inside the object, and

Hi, I want to change .RDA file to a text file. So I did as follows. >load("my.rda") >ls() ---> then it showed [1] exprs >write.table(exprs,"C:\\my.txt",sep="\t") I was successful with the first .RDA file. Then I used the same commands with another .RDA file (172 MB)which is 4 times bigger than the first file (41.2 MB). When I put the last command

Dear R-help Hi, I'm Won. I try to do microarray normalization by R. I use justRMA function within affy package, got error about segment fault. I don't know why it happen. I attached error below. Please help me. Thank you. Cheers, Won ======================= OS : Redhat linux Cpu : intel xeon X5570 Memory : 26Gb & OS : Ubuntu Cpu : intel q6600 Memory : 8Gb

Hi, I'm updating the LMGene package from Bioconductor. "Writing R Extensions" suggests that all source files (the ones in the R directory) have a .R ending, so I added it to the (one) source file. The next time I installed and ran R, R didn't understand any of the functions. I tried various things and eventually went back to the file and dropped the .R ending, installed, ran R.

Hello, I am using the following code to plot an MVA plot. library(affy) library(Biobase) library(limma) library(gcrma) pd<-read.phenoData("Clk.targets.2.txt",header=TRUE, row.names=1,as.is=TRUE,sep="\t") Data <- ReadAffy(filenames=pData(pd)$FileName,phenoData=pd) Print(Data) eset <- gcrma(Data) write.exprs(eset,

Hi, I'm running some routines with standard matrix operations like solve() and diag(). When I do a profile, the lead item under total time is standardGeneric(). Furthermore, solve() and diag() have much greater total time than self time. ??? I assume there is some time-consuming decision going on in the usual functions; is there any way to avoid that and go straight to the calculaions? Thanks

I changed the path to include C:\Program Files\R\R-2.3.1\bin, but Rcmd check [package] just returns an error: 'Rcmd' is not recognized as an internal or external command, operable program or batch file. Any ideas? I want to be able to compile this package on Windows. [[alternative HTML version deleted]]

Dear listers, After activating the name space for my bioconductor package (prada) I successfully ran R CMD check. However when loading the package in R and running the examples the imported function brewer.pal from package RColorBrewer is not found. I can directly call brewer.pal from the RColorBrewer name space typing RColorBrewer::brewer.pal, but it is not imported into my prada name space. When

Dear listers, After activating the name space for my bioconductor package (prada) I successfully ran R CMD check. However when loading the package in R and running the examples the imported function brewer.pal from package RColorBrewer is not found. I can directly call brewer.pal from the RColorBrewer name space typing RColorBrewer::brewer.pal, but it is not imported into my prada name space. When

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

Hello, I'm wondering how I can merge two featuresets into one. My dataset is two sets of microarray data and it looks like followings: > rawData $v1 TilingFeatureSet (storageMode: lockedEnvironment) assayData: 2197815 features, 59 samples element names: channel1, channel2 protocolData rowNames: LT290677RU_D1_2011-02-16 LT286300LU_D1_2010-07-24 ... LT003990RU_D1_2010-11-04 (59