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Analysis of Microarray Data Using S-PLUS, R and S+ArrayAnalyzer 23rd March 2006 Presenter: Adam Diaz Venue: Insightful UK, Network House, Basing View, Basingstoke, Hants RG21 4HG This is the last chance to register for this unique course being run by a member of Insightful's microarray development team from the US...

Hi: I have clustered microarray gene expression data and trying to map between microarray probe, gene, pathway, gene ontology, and homology for a set of (affy) microarray probes. Is there any package in R which facilitates this? I am looking at bioconductor, but till now could not find a solution. A link to some worked example wo...

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

Hey So sorry to be a total newbie, but i'm just finding my feet with R. I heard on the grapevine i could recreate a scanned microarray image, or at least get a good graphic of it from a just a data file. I have .txt files for illumina beadarrays but no images cos the service we used didn't send them. The 'beadarray' package seems to require TIFFs to get the graphic output. Does anone know of a way/a package i can use...

Hi, I am following the protocol outlined here for analysis of single channel Agilent microarray data: http://matticklab.com/index.php?title=Single_channel_analysis_of_Agilent_microarray_data_with_Limma I keep getting the following error message when using Limma's read.maimages function to load my data into an RGList object: Error in RG[[a]][, i] <- obj[, columns[[a]]] : number of...

Hi I am Aadhithya I am trying to write a code to classify microarray data (AML and ALL) using SVM in R my code goes like this : library(e1071) train<-read.table("Z:/Documents/train.txt",header=T); test<-read.table("Z:/Documents/test.txt",header=T); cl <- c(c(rep("ALL",10), rep("AML",10))); model<- svm(train,cl); p...

Dear maintainer, I used bioconductor package, pdInfoBuilder, to make a microarray platform annotation package. I named this package, pd.pdinfo.gpl11164.ndf.txt. This "self-made package" is to be used with oligo package. Prior to using oligo package, I need to install the annotation package, pd.pdinfo.gpl11164.ndf.txt, and cannot just copy it to the library tree. I...

Prof. Javier Cabrera will be giving the online course "DNA Microarray Data Analysis" from Jan. 28 - Feb. 25 at statistics.com. Dr. Cabrera is co-author of "Exploration and Analysis of DNA Microarray and Protein Array Data" (the course text; Wiley) and has published a number of articles on gene expression data analysis, data mining and multivariate...

Full_Name: Eric Libby Version: 2.1.1 OS: OS Tiger Submission from: (NULL) (65.93.158.117) I am trying to analyze microarray data of 42 human arrays. I typed in the following instructions: library(affy) Data <-ReadAffy() eset <- expresso(Data, normalize.method="invariantset", bg.correct=FALSE, pmcorrect.method="pmonly",summary.method="liwong") And I get some sort of memory error that...

Is there any package that allow you to perform "MA plot" like graph for Toray microarray data? Unlike Affymetrix CEL file which contain 2 values (R and G), Torray raw data only contain 1 value. MA-plot is Affymetrix specific which usually available for in (limma) package. P. Dubois [[alternative HTML version deleted]]

Hola, Quería preguntar si alguien conoce alguna referencia que pueda ayudarme a entender cuál es la mejor forma de lidiar con valores faltantes para aplicar svm en datos de microarrays. Estoy pensando que una buena solución es eliminar la variable en la que exista un valor faltante de la matriz de datos. En el paquete e1070 de R se elimina la muestra que contiene valores faltantes, pero eso para datos de microarrays implica eliminar miles de observaciones por un solo valor falta...

...cbind,lapply(1:400, function(i) {permutation<-sample(mydata4); (rowMeans(permutation[,1:27])-rowMeans(permutation[,28:38]))/(rowSds(permutation[,1:27])+rowSds(permutation[,28:38]))} )) ?dim(res) #[1]? 10 400 A.K. >I want to do permutation test and then get a PGC score 400 times on mydata4 (microarray data) > >I use 2 functions as below: >1. permutation<-sample(mydata4) >2. PGC <- (rowMeans(permutation[ ,1:27]) - rowMeans(permutation[ ,28:38]))/ (rowSds(permutation [,1:27]) + rowSds(permutation [,28:38])) > >What should I do to repeat these 2 functions in succession...

XLSolutions Corporation (www.xlsolutions-corp.com) is proud to announce: (1) Introduction to R/S+ programming: Microarrays Analysis and Bioconductor *** San Francisco / July 17-18, 2006 *** *** Chicago / July 24-25, 2006 *** *** Baltimore / July 27-28, 2006 *** *** Raleigh / July 17-18, 2006 *** *** Boston / July 27-...

3rd Millennium is announcing the release of its award winning Array Repository and Data Analysis System (ARDAS) version 2. ARDAS is a web-enabled enterprise software system that provides a complete and fully integrated solution to microarray data acquisition, management, and analysis. ARDAS includes three main modules: 1- A Laboratory Information Management System (LIMS) 2- A repository and data warehouse 3- An Analysis Information Management System (AIMS) based on bioconductor and R ARDAS is a robust and scalable enterprise system b...

Hi, I am beginning to learn R and have a data table that I would like to produce a microarray-like plot. The table looks like this: 3 0 0 3 -377.61 1.94 3 0 0 3 -444.80 2.36 2 1 0 3 -519.60 2.39 1 1 1 3 -54.88 2.49 2 1 1 4 -536.55 2.53 1 0 1 2 108.29 2.62 2 0 0 2 39.56 2.62 3 0 1 4 108.32 2.63 2 0 0 2 -455.23 2.84 1 0 0 1 -432.30 2.98 ... I would like to assign colors to the first three c...

Dear Listers: Currently I am doing a research using a microarray data. I have two questions and hope I can get some help from here: 1. I have a dataset like the following, in which V1 is geneid, v3...are the fold changes of expression levels for different patients. There are multiple probes for one gene, so there are multiple rows. You can see from column V11 a...

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3rd Millennium is announcing the release of its award winning Array Repository and Data Analysis System (ARDAS) version 2. ARDAS is a web-enabled enterprise software system that provides a complete and fully integrated solution to microarray data acquisition, management, and analysis. ARDAS includes three main modules: 1- A Laboratory Information Management System (LIMS) 2- A repository and data warehouse 3- An Analysis Information Management System (AIMS) based on bioconductor and R ARDAS is a robust and scalable enterprise system b...

Dear All: Significance Analysis of Microarrays(SAM) As we know sam do multiple t.test as following ## Default S3 method: t.test(x, y = NULL, alternative = c("two.sided", "less", "greater"),mu = 0, paired = FALSE, var.equal = FALSE,conf.level = 0.95, ...) var.equal: a logical variable indicating whether to treat...

For any given pre-specified gene or short list of genes, yes the Cox model works fine. Two important caveats: 1. Remeber the rule of thumb for a Cox model of 20 events per variable (not n=20). Many microarray studies will have very marginal sample size. 2. If you are looking at many genes then a completely different strategy is required. There is a large and growing literature; I like Newton et al, Annals of Applied Statistictis, 2007, 85-106 as an intro; but expect to read much more. Terry Thernea...