search for: expressionset

...OCALS~1\\Temp\\RtmpXrUE8T\\file2ea6bb3" > eSet <- read.exprSet(testFile) Warning messages: 1: read.exprSet is deprecated, use readExpresionSet instead 2: read.phenoData is deprecated, use read.AnnotatedDataFrame instead 3: The phenoData class is deprecated, use AnnotatedDataFrame (with ExpressionSet) instead 4: The exprSet class is deprecated, use ExpressionSet instead 5: The exprSet class is deprecated, use ExpressionSet instead 6: The exprSet class is deprecated, use ExpressionSet instead 7: The exprSet class is deprecated, use ExpressionSet instead 8: The exprSet class is deprecated, u...

...propriate 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") > library("Biobase") > data(sample.ExpressionSet) > class(sample.ExpressionSet) [1] "ExpressionSet" attr(,"package") [1] "Biobase" > z <- featureNames(sample.ExpressionSet) > z[1:2] [1] "AFFX-MurIL2_at" "AFFX-MurIL10_at" > ?featureNames(sample.ExpressionSet) Warning message: no met...

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: subset.ExpressionSet <- function(x,subset,...){ } I will use the subset argument for rows (genes), as in default method. Now I would like to allow to select differe...

...; 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") > >> library("Biobase") >> data(sample.ExpressionSet) >> class(sample.ExpressionSet) > [1] "ExpressionSet" > attr(,"package") > [1] "Biobase" >> z <- featureNames(sample.ExpressionSet) >> z[1:2] > [1] "AFFX-MurIL2_at" "AFFX-MurIL10_at" >> ?featureNames(sample.Ex...

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.

...e. 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 believe I have enough RAM and disk spa...

...s. str() / attributes() to probe inside the object, and something@something$something to walk it and explore. Is there any other way? Also, without reading documentations, is there a way to know what functions are available to extract data from it? For example, there is sampleNames() which works on ExpressionSet and AnnotatedDataFrame (which is a part of ExpressionSet). How do I know they are available (as sometimes I can't recall where I've seen them and I forgot the function names). And what are R functions? Are those two separate functions or polymorphic functions? I'm also pretty confused a...

...tory material. To view, type 'openVignette()' or start with 'help(Biobase)'. For details on reading vignettes, see the openVignette help page. Loading required package: affyio > getMethods("geneNames") An object of class ?MethodsList? Slot "methods": $ExpressionSet Method Definition: function (object) { .Deprecated("featureNames") featureNames(object) } <environment: namespace:Biobase> Signatures: object target "ExpressionSet" defined "ExpressionSet" $exprSet Method Definition: function (objec...

...tialize 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) instead Can someone suggest me how to use the new method AnnotatedDataFrame to create eSet? Thanks Manisha [[alternative HTML version deleted]]

...of .CEL etc extension, just keep GSM } } if(!exists("affyobj")){ mdExprs <- as.matrix(read.csv(defaultExprs,row.names=1)) if( min( mdExprs, na.rm = TRUE ) >= 0 & max( mdExprs, na.rm = TRUE ) >= 50 ) { mdExprs <- log(mdExprs, base = 2) } affyobj <- new("ExpressionSet",exprs=mdExprs) } x <- arrayQualityMetrics(expressionset = affyobj, outdir=qcDir, force = TRUE, spatial=FALSE) [[alternative HTML version deleted]]

...this seems to be more general: https://stat.ethz.ch/pipermail/bioc-devel/2013-May/004311.html See reproducible example from Martin below. Thank you. Renaud ---------- Forwarded message ---------- From: Martin Morgan <mtmorgan at fhcrc.org> Date: 7 May 2013 19:55 Subject: Re: [Bioc-devel] ExpressionSet and LumiBatch: inheritance problem in S4 methods for union class To: Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za> Cc: bioc-devel at r-project.org, dupan.mail at gmail.com I can replicate this with a simpler example, where PkgA has setClass("A", representation(x="numeri...

Hello: Is there a way to get a mean from values stored in different rows? The data looks like this: YEAR-1, JAN, FEB, ..., DEC YEAR-2, JAN, FEB, ..., DEC YEAR-3, JAN, FEB, ..., DEC What I want is the mean(s) for just the consecutive winter months: YEAR-1.DEC, YEAR-2.JAN, YEAR-2.FEB YEAR-2.DEC, YEAR-3.JAN, YEAR-3.FEB etc. Thanks.

Hi, I m not able to plot normalized data(normalization by rma) using boxplot. I don't know why? basically, object(formed of normalized data) belong to ExpressionSet class. It is showing error Error in x[!xna] : object of type 'S4' is not subsettable In addition: Warning messages: 1: In is.na(x) : is.na() applied to non-(list or vector) of type 'S4' 2: In is.na(x) : is.na() applied to non-(list or vector) of type 'S4' Now, how to plo...

Hi all,   I have loaded the LIMMA and Biobase package and tried these commands:   library(limma) library("Biobase") data <- read.table("c:/temp/data.txt",header=T,row.names=1) ExpressionData <- as.matrix(data[,c(2,3,4,6,7,8)]) eset <- new("ExpressionSet", exprs = ExpressionData) design <- cbind(WT=1,P=c(0,1,1,0,1,1),G=c(0,1,0,0,1,0)) fit <- lmFit(eset,design)   But I keep getting an eroor message after "lmFit" that says: Error in possibleExtends(cl, class2, class1Def, class2Def) : trying to get slot "subclasses" fr...

Full_Name: Guy W. Tillinghast Version: 2.8.0 OS: Windows XP professional Submission from: (NULL) (24.248.24.3) I am encountering difficulty asking R to manipulate the correct columns in Expression Set class (object 4). I download the ALL data with: library(golubEsets) data(Golub_Merge) Note, the data has the samples not in order. This is not R's fault (at least not that I can tell): >

Hello All, I need your help. I am analysing affymetrix data and have to select the probe-set that has median expression among all the probe-sets for same gene. This way I want to remove the redundancy by keeping the analysis to single gene entry level. I am fully aware that it is not a nice thing to do but I just have to do it. To do so, I came across 'findLargest' function of

...sts("affyobj")){ >> mdExprs<- as.matrix(read.csv(**defaultExprs,row.names=1)) >> if( min( mdExprs, na.rm = TRUE )>= 0& max( mdExprs, na.rm = TRUE )>= 50 >> >> ) { >> mdExprs<- log(mdExprs, base = 2) } >> affyobj<- new("ExpressionSet",exprs=**mdExprs) >> } >> >> x<- arrayQualityMetrics(**expressionset = affyobj, >> outdir=qcDir, >> force = TRUE, >> spatial=FALSE) >> >> [[alternative HTML vers...

...----- Errors also show in the terminal as below, ------------- > Error: no function to return from, jumping to top level In addition: Warning messages: 1: read.phenoData is deprecated, use read.AnnotatedDataFrame instead 2: The phenoData class is deprecated, use AnnotatedDataFrame (with ExpressionSet) instead Error in exprs(RawAffyData) : no function to return from, jumping to top level -------------- I'm running R version 2.6.1 under Linux Ubuntu 7.10 -------------- My sessionInfo is shown below, -------------- > sessionInfo() R version 2.6.1 (2007-11-26) i486-pc-linux-gnu...

...omal information 5: annotate - HOWTO: Use the online query tools 6: annotate - Using Affymetrix Probe Level Data 7: annotate - Using Data Packages 8: annotate - Using the homology package 9: AnnotationDbi - AnnotationDbi 10: AnnotationDbi - SQLForge 11: Biobase - An introduction to Biobase and ExpressionSets 12: Biobase - Bioconductor Overview 13: Biobase - esApply Introduction 14: Biobase - Notes for eSet developers 15: Biobase - Notes for writing introductory 'how to' documents 16: Biobase - quick views of eSet instances 17: geneplotter - How to assemble a chromLocation object 18: geneplotte...

...biol %in% c(BCR/ABL, NEG), ] : > >> error in evaluating the argument 'i' in selecting a method for function '[': Error in c(BCR/ABL, NEG) : unused argument(s) (NEG) At this point, I really appreciate any inputs to move forward. ?. > str(ALL) > Formal class 'ExpressionSet' [package "Biobase"] with 7 slots > ..@ experimentData :Formal class 'MIAME' [package "Biobase"] with 13 slots > .. .. ..@ name : chr "Chiaretti et al." > .. .. ..@ lab : chr "Department of Medical Oncology, Da...