similar to: wolfinger microarray normalization

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, I have a linear mixed-effects model object and want to extract the 95% confidence intervals for the fixed and random effects, respectively. I found the function intervals() for confidence intervals for the fixed effects but no corresponding function for the random effects. Does it exist or do I have to calculate the confidence intervals for the random effects myself? Greetings, joerg

Hi, does anybody know of a nice test to detect trend turning points in time series? Possibly with reference? Thanks, joerg

Hi, I have two non-normal distributions and use interquartile ranges as a dispersion measure. Now I am looking for a test, which tests whether the interquartile ranges from the two distributions are significantly different. Any idea? Thanks, joerg [[alternative HTML version deleted]]

Hi, trying to do a robudt regression of a two-way linear model, I keep getting the following error: > lqs(obs ~ y + s -1,method="lms", contrasts=list(s=("contr.sum"))) Error: lqs failed: all the samples were singular Robust regression with M-estimators works (also regular least square fits, of course): rlm.formula(formula = obs ~ y + s - 1, method = "M",

Hello, Situation: We are in a school class every student logs on with the same account. Until now we had Shares that were accessable for everybody and it was therefore possible to look into and edit/delete other's files. Plan: Create a share that can be clicked on which then asks for User/Pass and directly maps to the User's home Directory upon auth. User auth is done through LDAP

Dear R-Tech Support Team, I was just browsing on your web page and I am curious about R's system requirements. How many MB RAM and what processor speed would you recommend for Win XP if I want to load QuantArray Excel output files of appr. 16 MB each? Thank you very much in advance, Derk Bemeleit ----------------------------------------------- A--------T T-------A Dipl.-Biol.

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. Extract Microarray technology is complex, and experiments using

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

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 methods in leading

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]]

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); pred <-

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 would be appreciated. Thanks and regards. John [[alternative HTML

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

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

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

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 columns

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 and V13, the fold changes are very

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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