search for: exprset

...array 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 <- tempfile() >textAffy<-read.table("textE_to_affy.csv",header=TRUE,sep=",",row.names=1) > textAffy Sample1 S...

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 at Nabble.com.

...uccessful 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 (write.table), it showed as below. Error: cannot allocate vector of size 92.8 Mb In addition: Warning messages: 1: The exprSet class is deprecated, use ExpressionSet instead 2: The exprSet class is deprecated, use ExpressionSet instead 3: The exprSet class is deprecated, use ExpressionSet instead 4: The exprSet class is deprecated, use ExpressionSet instead What could be a problem in this case? Is it the memory problem? I...

Hi list, I have a question about using *read.table()* to read in a txt file. Basically, it consists of 16346 rows, 6 columns (no header). The code I used is: exprSet <- read.table('process_all4_GSA2.txt', row.names = 1,header =FALSE) and I got an error message: > exprSet <- read.table('process_all4_GSA2.txt', row.names = 1,header =FALSE) Error in read.table("process_all4_GSA2.txt", row.names = 1, header = FALSE) : duplicat...

...ses loads Biobase, and when explicitly done, as in library(Biobase) library(marrayClasses) is fine, but when Biobase is loaded via a require statement in marrayClasses' .First.Lib, I end up with: Warning message: In the method signature for function "coerce", class "exprSet" has no current definition in: matchSignature(signature, fdef, where) and based on the "band-aid" working above, suggests an initialization or evaluation timing problem. (and exprSet is defined in the Biobase package). best, -tony -- rossini@u.washington.edu http:/...

...t? Slot "methods": $ExpressionSet Method Definition: function (object) { .Deprecated("featureNames") featureNames(object) } <environment: namespace:Biobase> Signatures: object target "ExpressionSet" defined "ExpressionSet" $exprSet Method Definition: function (object) featureNames(object) <environment: namespace:Biobase> Signatures: object target "exprSet" defined "exprSet" Slot "argument": object Slot "allMethods": $ExpressionSet Method Definition: function (ob...

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...der =TRUE,row.names=1); colnames(pd) <- c("type","tumor","time","id"); pdN <- list(type = "Cellline/xenograft",tumor="primary,secondary,cellline",time = "0hr,1hr,2hr,4hr", id = "1,2,3,4,5,6,7,8,9") # Initialize exprSet object pD <- new("phenoData", pData=pd, varLabels=pdN); # This is my eSet!!! metastasis.eset <- new("exprSet", exprs=as.matrix(geneExpr.log), phenoData=pD) I get the following error: The phenoData class is deprecated, use AnnotatedDataFrame (with ExpressionSet)...

...s include: \begin{itemize} \item \texttt{GSload.int()} - Read GeneSpring experiment interpretation from file and return a GeneSpring gene expression object (GSint) \item \texttt{GSload.intBC()} - Read GeneSpring experiment interpretation from file and return a BioConductor gene expressioon object (exprSet) \item \texttt{GSload.exp()} - Read GeneSpring experiment from file and return a GeneSpring gene expression object (GSint) \item \texttt{GSload.expBC()} - Read GeneSpring experiment from file and return a BioConductor gene expressioon object (exprSet) \item \texttt{GSint()} - Create a GeneSpring ge...

...ows (genes) and 65 columns (samples). I did unsupervised clustering using pvclust to get 4 classes. What I would like to do is to get unique genes for each class which can best characterize them. I did so and had the problem when running the code. The error message is: > rf.vs1 <- varSelRF(exprSet, cl, ntree = 200, ntreeIterat = 100, vars.drop.frac = 0.2) error in randomForest.default(x = xdata, y = Class, ntree = ntree, mtry = mtry, : length of response must be the same as predictors My code is: library(varSelRF) exprSet <- as.matrix(read.table('varSelRF_x.txt',header...

...for using the capitalizations to make code more self explanatory, but only if a consistent system is used. In Java, capitalization is used to indicate the type of object. Names of methods are capitalized except for the first word (e.g., geneNames), names of classes are fully capitalized (e.g., ExprSet), names of data objects are all lowercase, and names of libraries have their own conventions but normally with lowercase letters. A programmer can recognize the type of object in many cases simply from the name. In R, Java capitalization has started to be used for formal generic functions, but...

....3 in BioC CVS.) Depending on how both packages are loaded, the Biobase definitions seem to be getting masked out: > library(Biobase) > library(annaffy) > showMethods("[") Function "[": x = "ANY" x = "container" x = "phenoData" x = "exprSet" x = "aafList" x = "aafTable" > library(annaffy) (annaffy loads Biobase in .First.lib) > showMethods("[") Function "[": x = "ANY" x = "aafList" x = "aafTable"

...n measures. * AnnBuilder: DB support is no longer required. ABPkgBuilder now provides a signle API for building of data packages. Also, data packages built with AnnBuilder will include an evidence code and association information for GO ids. * Biobase: The exprs2excel method for the exprSet class has been added, which will create an excel friendly file from the expression component of an exprSet. * DynDoc: A new package that provides a set of functions to create and interact with dynamic documents and vignettes * limma: A new package that provides functionality to hand...

Dear List, I have a data matrix that consists of ~4500 rows and 25 columns (i.e. an exprSet object that I converted via the 'exprs' function into a data matrix) Now I want to remove/delete the rows where all exp. values in that particular row are below or equal to a specific cut-off value (e.g 1.11) I have tried using several commands to address this issue: >Matrix[rowSums(Ma...

Hi How do I install "gregmisc" packages? I did- % sudo R > install.packages("gregmisc") . . > barplot2() but, Error: couldn't find function "barplot2" -- atuya Mac OSX 10.2.6 R 1.7.1

...fymetrix annotation data packages. Produces compact HTML and text reports including experimental data and URL links to many online databases. Allows searching biological metadata using various criteria. --- Biobase: The generic function as.data.frame() now works on objects of class exprSet. This lets one access the extensive modeling facilities through formula offered by R and packages like 'nlm'. --- factDesign: A package containing functions useful for analyzing data from factorial designed microarray experiments. --- gpls: Classification using partial leas...

...fymetrix annotation data packages. Produces compact HTML and text reports including experimental data and URL links to many online databases. Allows searching biological metadata using various criteria. --- Biobase: The generic function as.data.frame() now works on objects of class exprSet. This lets one access the extensive modeling facilities through formula offered by R and packages like 'nlm'. --- factDesign: A package containing functions useful for analyzing data from factorial designed microarray experiments. --- gpls: Classification using partial leas...

...tion via the limiting distribution and conditional Monte-Carlo procedures are available for every test while the exact null distribution is currently available for two-sample problems only. Inference problems can be specified by a traditional formula based interface. Support for data available as `exprSet' objects in a BioC environment is implemented as well. The theoretical framework is sketched in the vignette and we refer to `vignette("coin")' for further details. Comments, suggestions, bug-reports etc. are more than welcome! Best, Torsten, Kurt, Mark and Achim _____________...

...tion via the limiting distribution and conditional Monte-Carlo procedures are available for every test while the exact null distribution is currently available for two-sample problems only. Inference problems can be specified by a traditional formula based interface. Support for data available as `exprSet' objects in a BioC environment is implemented as well. The theoretical framework is sketched in the vignette and we refer to `vignette("coin")' for further details. Comments, suggestions, bug-reports etc. are more than welcome! Best, Torsten, Kurt, Mark and Achim _____________...

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,