similar to: Limma B-statistics

I am having trouble converting the output from Sweave into a valid PDF file. I have created a simple .Rnw file which will become a full vignette at some point, but during the intermediate testing, I got errors from texi2dvi. This is what I have done. 0) Using a Windows Xp system 1) Created a file called GeneSpring.Rnw 2) Convert this to Tex using Sweave("GeneSpring.Rnw") from within R

Greetings! The Bioconductor core group would like to announce the 5th release of Bioconductor, version 1.4. There are many new packages as well as several major upgrades and fixes in older packages, and users are encouraged to upgrade existing tools and check out the new packages. Release 1.4 is intended to be operated with R version 1.9.x, which can be obtained at CRAN

Dear list members, I am analysing my microarray data using limma package. Now I encounter several problems. Looking forward to your suggestions! Question 1: During the process of background correction using method="normexp", four warning messages appeared as "NaNs produced in: log(x)" (as you can see in the program posted below). What does that mean? How will it effect the

On Wed, December 22, 2004 12:11 am, r.ghezzo at staff.mcgill.ca said: > ----- Forwarded message from r.ghezzo at staff.mcgill.ca ----- > Date: Mon, 20 Dec 2004 15:45:11 -0500 > From: r.ghezzo at staff.mcgill.ca > Reply-To: r.ghezzo at staff.mcgill.ca > Subject: [R] problems with limma > To: r-help at stat.math.ethz.ch > > I try to send this message To Gordon

I try to send this message To Gordon Smyth at smyth at vehi,edu.au but it bounced back, so here it is to r-help I am trying to use limma, just downloaded it from CRAN. I use R 2.0.1 on Win XP see the following: > library(RODBC) > chan1 <- odbcConnectExcel("D:/Data/mgc/Chips/Chips4.xls") > dd <- sqlFetch(chan1,"Raw") # all data 12000 > # > nzw <-

Hi Everyone, I have been trying to read some Arrayvision files( 2 channel cDNA) and am having some problem. My code is : setwd('C:/work/data/limma/ndd1'); files <- c('ndd1_1.txt','ndd1_2.txt','ndd1_3.txt'); RG=read.maimages(files,"arrayvision",sep="\t"); #Normalisation MA=normalizeWithinArrays(RG); #plotPrintTipLoess(MA); #Fit Linear

Hi, I am a Ph.D. student from Québec, Canada. I’m a beginner with R and Bioconductor. Until now the only experience I have is in analyzing microarray data using affy and limma packages. Now I am trying to analyze Rat Gene 10 st arrays and I would like to run RMA analysis and Smyth moderated t test on those arrays. Since no cdf official package is available for those arrays, after reading many

Dear All, I am using the LIMMA package to create 2 contrasts for my data and then calculating the vennCounts of the decideTests from the contrast.fit to be able to create venn Diagrams. The code works fine but the summary(results) shows zeros for all i.e. no gene were up regulated or downregulated. This is not true for my data since toptable output shows Log fold change greater than > 2. I am

Dear R-Help, I am using the function "topTable" from the LIMMA package. To estimate adjusted P-values there are several options (adjust="fdr" , adjust="BH") as shown below: topTable(fit, number = 10, adjust = "BH", fit$Name) I guess any of these options (fdr, BH, etc.) is using a default of FDR=0.05 which is quite conservative (i.e., very

Hello, I have just completed an analysis of microarray data using the limma package. The analysis appears to have worked fine. However, when I use the topTable function to get the significant genes, I get the following error: > topTable(fit2,coef=5,adjust="fdr") Error in array(x, c(length(x), 1), if (!is.null(names(x))) list(names(x), : attempt to set an attribute on NULL

I'm new to this site so I hope this isn't too naive a problem. I'm trying to use the permax function with a data frame containing gene expression measurements taken from 79 microarray experiments with >3000 genes per array. The data contains missing values and every time I use permax with the data frame I get the error: NA/NaN/Inf in foreign function call (arg 1) Could anyone

Hi, I have a question concerning the analysis of some affymetrix chips. I downloaded some of the data from GEO GSE11324 (see below). In doing so I'm stuck after I identified the probesets with significant changes. I have problems in assigning probeset specific gene names as well as getting the genomic coordinates. Furthermore I have no clue how to deal with the fact, that most genes have

Hi all, My name is Amy, I am a masters student in Bioinformatics at North Carolina State University. I am working on a project and I am trying to use the lumi R package for microarray data analysis. I have shown the sample code here and have questions about modifying the sample code for my own data. lumi package in R, example.lumi, the sample data has 8000 features and 4 samples I have

Dear Sirs, How can I revert to an older limma version? Typing "install.packages("limma")" in R gives a list of mirrors. How can I install the version I want after I obtain and untar the file (e.g, limma_2.9.1.tar.gz)? I am running R 2.5.0 on a Linux machine (CentOS 5). When using limma it will not go past the read.maimages command. I get this error: Error in

Dear All, How to cite the PDF user's guide for the LIMMA package? This is not about how to cite the LIMMA package. Roger Roger L. Vallejo, Ph.D. Computational Biologist & Geneticist U.S. Department of Agriculture, ARS National Center for Cool & Cold Water Aquaculture 11861 Leetown Road Kearneysville, WV 25430 Voice: (304) 724-8340 Ext. 2141 Email: roger.vallejo@ars.usda.gov

Hi all. I've got a really dumb question for anyone. How do I write the output of a limma analysis (basically the topTable) to a text file? I want to output the topTable for the entire microarray (not really a topTable anymore I suppose..). Thanks for any advice! -Josh

I have a very basic question about limma. Assume I have experiments from 3 or more RNA sources in a reference design. It is easy to define individual contrasts but I want to specify a contrast matrix that tests for significant differences among ALL the different RNA sources (i.e. the analogous thing to a simple One-Way ANOVA). How can I do that? Thanks! Max --

Hi all, My name is Amy, I am a masters student in Bioinformatics at North Carolina State University. I am working on a project and I am trying to use the lumi R package for microarray data analysis. I have shown the sample code here and have questions about modifying the sample code for my own data. lumi package in R, example.lumi, the sample data has 8000 features and 4 samples I have

Dear R-Help, I am using the LIMMA User's Guide 5 January 2007 PDF version. For the example show in Section 7.4 DIRECT TWO-COLOR DESIGNS (pgs. 33-34), I could not grasp the rationale in developing the contrast.matrix with these R statements (">" indicates the R command prompt): > contrast.matrix <-

Hi, I have a question about limma. I have data from spotted arrays. I have class A and Class B on the same slide. In Limma if I put class A as the reference (ref), are the list of genes I get in the output for class A or class B? #design <- modelMatrix(targets, ref="classA") design Josephine Brennan [[alternative HTML version deleted]]