similar to: LIMMA decideTests result zero from contrast matrix

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

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,when I perform SAM on my array data(siggenes)I have some problems in retrieving the separate lists of up regulated and down regulated genes. When I write: fold<-function(x){ gruppi<-split(x,controllo) geni1<-abs(mean(gruppi[[2]])-mean(gruppi[[1]])) return(geni1) } fold<-esApply(expr.contr.tratt.4,1,fold)

Hi! The Netfilter project proudly presents: libnftnl 1.0.7 libnftnl is a userspace library providing a low-level netlink programming interface (API) to the in-kernel nf_tables subsystem. The library libnftnl has been previously known as libnftables. This library is currently used by the nft command line tool. This release includes the following list of updates: * New nftnl_rule_cmp()

Hi! The Netfilter project proudly presents: nftables 0.7 This release contains many accumulated bug fixes and new features available up to the (upcoming) Linux 4.10-rc1 kernel release. * Facilitate migration from iptables to nftables: At compilation time, you have to pass this option. # ./configure --with-xtables And libxtables needs to be installed in your system. This allows

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 <-

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

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]]

Hi, I need some help with the interpretation of B statistics generated by eBayes in the limma package. I want to compare gene expression in three groups of Affy samples. The expression set has been imported from GeneSpring using GSload.expBC and a linear model fitted to the data using a design based on the three groups (6, 5, and 5 samples in each group, respectively). I have then made 3

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

Hi all, I'm working on microarray and currently analyzing the microrarray data using limmaGUI. Loop design has been applied in this experiment. This is a 2X2 factorial experiment where there are control and treatment at 2 different time points, week 6 and 9. The experimental design is almost the same as the limmaGUI work example: Weaver Data set. I would like to look at the effect of

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

Hello Limma users A quick question, I hope: I have dual-channel spotted expression arrays in a simple loop design (no dye swaps), viz: 1 vs reference 2 vs 1 3 vs 2 reference vs 3 There are 4 replicate spots for each probe on each array. It seems as if getting meaningful spot summary results using duplicateCorrelation() is not possible in my case as the spots are not regularly spaced, and I

Hello listmemebers, I have data from two-color microarray expression profiling experiments where 3 whole brain (WB) samples were compared to 3 Mauthner Cells (MC) in a loop design (-> MC #1 -> WB #1 -> MC #2 -> WB #2 -> MC #3 -> WB #3 -> MC #1 ->). In addition to phenotype analysis I would also like to run an individual analysis making all pair-wise comparisons. I'm

https://bugzilla.netfilter.org/show_bug.cgi?id=1248 Bug ID: 1248 Summary: The rr-load-balance part doesn't actually work on 0.7 Product: nftables Version: unspecified Hardware: x86_64 OS: All Status: NEW Severity: minor Priority: P5 Component: nft Assignee: pablo at

I am posting this to both R and BioC communities because I believe there is a lot of confusion on this topic in both communities (having searched the mail archives of both) and I am hoping that someone will have information that can be shared with both communities. I have seen countless questions on the BioC list regarding limma (Bioconductor) and its calculation of FDR. Some of them involved

I am posting this to both R and BioC communities because I believe there is a lot of confusion on this topic in both communities (having searched the mail archives of both) and I am hoping that someone will have information that can be shared with both communities. I have seen countless questions on the BioC list regarding limma (Bioconductor) and its calculation of FDR. Some of them involved

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 have two data set of normalized Affymetrix CEL files, wild type vs Control type.(each set have further three replicates). > wild.fish AffyBatch object size of arrays=712x712 features (10 kb) cdf=Zebrafish (15617 affyids) number of samples=3 number of genes=15617 annotation=zebrafish notes= > Dicer.fish AffyBatch object size of arrays=712x712 features (10 kb) cdf=Zebrafish (15617

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