Bioconductor Forum

<div class="preformatted">Dear Atul, There are a million ways to add columns of annotation. For example, you could add the Intensities to the gene annotation data.frame: fit2$genes <- data.frame(fit2$genes,Intensities) so that the intensities will appear in any output table from limma. Best wishes Gordon ----------- original email --------------- [BioC] Limma/Affy - Include …

Annotation limma Annotation limma

updated 12.7 years ago • Gordon Smyth

I am working with two-colour data generated by Imagene image analysis. I encountered a problem in limma 2.4.9 I try to read in intensity data (according to the User's guide section 4.4) like this: > targets<-readTargets() &gt...stats" "graphics" "grDevices" "utils" "datasets" [7] "base" other attached packages: limma "2.4.9" Best, Georg </div

limma limma

updated 19.9 years ago • Georg Otto

Morten, > > Thank you for your answer, but I am still not sure based upon it. > In Limma log2 is used for absolute intensities, and for M. > M=log2(Intenisity2)-log2(Intensity1). In limma, B and M appear in > the

limma limma

updated 19.7 years ago • Darlene Goldstein

in and do normalization of cDNA microarray data with format as .txt or .xls by marray package or limma. > > Yes, you should be able to read in the data if it is in .txt format. You can save the .xls files in tab delimited text format...delimited). Once you have the files in tab delimited text format, the function read.maimages() in limma can be used to read in the data, provided …

Normalization limma marray Normalization limma marray

updated 21.8 years ago • Matthew Ritchie

<div class="preformatted">> Date: Mon, 23 Jan 2006 14:02:03 -0800 > From: "Kathryn V. Steiger" <ksteiger at="" illumigen.com=""> > Subject: [BioC] limma control spot weights and normalization > To: <bioconductor at="" stat.math.ethz.ch=""> > > Will setting control spots to zero affect normalization within/among > arrays? Yes. no…

Normalization limma convert Normalization limma convert

updated 20.0 years ago • Gordon Smyth

div class="preformatted">I would like to place 2 venn diagrams generated by limma on single page. However they are very squeezy and there are much empty space above and below them. The output is attached...retaining their aspect ratio. I tried reducing oma to 0 but unable to get what I want. library("limma") Y <- matrix(rnorm(100*6),100,6) Y[1:10,3:4] <- Y[1:10,3:4]+3 Y[1:20,5:6…

hgu133a limma hgu133a limma

updated 16.8 years ago • Daren Tan

Hi,  I only noticed this by chance, but it peaked my curiosity and couldn't find any documentation about it. I occasionally get asked about experiments where conditions are in singlet (no replication), and my typical mandate is to run the line of "no replication, no statistics", however in the case of making the most of data available, I was aware of DESeq2's single sample method in whi…

limma

updated 8.3 years ago • andrew.j.skelton73

<div class="preformatted">Dear Norman / all, Many thanks for making PLGEM available to the community. It's a very straightforward package to use. I'm using this for spectral counts measured on four conditions. As far as I understand, PLGEM can fit the model to one comparison of interest at a time (Control_vs_condirion1, control_vs_condition2, ...) to detect differential expression. . I'm w…

limma plgem limma plgem

updated 14.3 years ago • Amin Moghaddasi

Hello, I'm getting a strange v-shaped volcano plot from limma. The data matrix is small - 400 observations, for two conditions - cond1, cond2,cond2 (so only have replicate for cond2). The

limma volcano plot

updated 8.7 years ago • yul

<div class="preformatted">Dear Dr. Smyth. Would you be that kind to help me on deciding whether yes or no to filter my microarray data set with a filtering method correcting for variance such as I/NI method from Talloen et al. (2007). Whereas many researchers say that filtering should increase the power of the test, then increasing the chance to get true deferentially expressed genes. Howe…

Microarray limma Microarray limma

updated 12.6 years ago • Garcia Orellana,Miriam

div class="preformatted">Dear Bioconductor List, I am using limma to fit a linear model with what I believe is called a disconnected design: > data <- ReadAffy() > eset<-rma(data) > design

Cancer limma Cancer limma

updated 18.7 years ago • Richard Friedman

gt;Subject: [BioC] limma 2.2.0 - decideTests heirarch/nestedF + BH correction >, small bug >Cc: Bioconductor >Date: Thu, 24 Nov 2005 14:51:34 +1100...gt; >>[BioC] limma 2.2.0 - decideTests heirarch/nestedF + BH correction , small bug >>Ariel Chernomoretz ariel.chernomoretz at crchul.ulaval.ca...70 ) > >On the other han…

limma limma

updated 20.1 years ago • Gordon Smyth

bioconductor="" pipermail="" stat.ethz.ch=""> -------------- next part -------------- library(limma) library(vsn) # DATA PREPROCESSING # Download RAW data from GEO experiment setInternet2(use=FALSE) download.file('http...design) fit2.vsn <- contrasts.fit(fit.vsn, contrast.matrix) fit3.vsn <- eBayes(fit2.vsn) limma::volcanoplot(fit3.vsn) RG$printer$ngrid.r = 1 imageplot(log2(RG.…

Microarray Normalization vsn limma ASSIGN Microarray Normalization vsn limma ASSIGN

updated 12.1 years ago • Marcin Jakub Kamiński

As Naomi Altman as already told you, analysing an experiment such as this is straightforward with limma. I guess the problem you are having is that you are trying to use the limma User's Guide's suggestion of forming a composite...Naomi and list, >> >> some time ago I asked a question on how to model an experiment in limma. >> I think I need some additio…

affy limma siggenes factDesign maanova affy limma siggenes factDesign maanova

updated 16.7 years ago • Gordon Smyth

Hi, Has anyone any experince of extracting the beta coefficients form a limma object (i.e. fit_2) and calculating the 5% and 95% confidence intervals for the coefficients? Any help would be hugely appreciated...ls") # Use this line for full run, hash out for testing fit_2 <- eBayes(fit) table <- limma::topTable(fit_2, coef = 2, number = Inf) Thanks, Matt

limma limmaGUI beta

updated 3.5 years ago • fluentin44

I am new to microarray data analysis. Please evaluate the following code for  block analysis in Limma and let me know about whether this code is appropriate??. library(limma) eset<-read.table("RMANormData_apap.txt") design

Microarray limma Microarray limma

updated 14.4 years ago • suri ghani

Where in the limma package's directory are the unit tests located? Are they all in one file

limma

updated 4.4 years ago • brianebrahimi

and it has recommendations for how to import data for downstream analysis in edgeR, DESeq2 and limma-voom, but it does not mention the lesser-used limma-trend. The edgeR method stores the length corrections in y$offset, but...doesn't use y$offset either. So am I correct in assuming that I should use the tximport method for limma-voom, but then should use cpm() instead of voom()? Thanks, Jenny

tximport limma limma-trend edgeR

updated 8.3 years ago • Jenny Drnevich

Dear Yanyan You can use the method described in Section 8.2 (Technical Replication) of the Limma User's Guide. Best wishes Gordon >Message: 9 >Date: Fri, 01 Dec 2006 11:52:37 -0500 >From: Yanyan Li <yli at="" mail.jci.tju.edu...gt;Subject: [BioC] Limma with block and replicate measurement >To: bioconductor at stat.math.ethz.ch >Message-ID: <5.2.0.9…

limma limma

updated 19.1 years ago • Gordon Smyth

other differences. In the latest versions of the packages, marrayNorm uses span=0.4 by default while limma uses span=0.3. This would easily produce the difference you see. (No doubt you have already checked the documentation...for such an obvious cause as this.) Other very small differences arise because limma uses lowess when there aren't any weights and loess when there are, while marrayNorm us…

Normalization limma Normalization limma

updated 22.4 years ago • Gordon Smyth

div class="preformatted">Fellow Expressionists, Does Limma automatically perform a multiple comparison adjustment for non-orthogonal contrasts? If not, can you recommend another...program that can be used in conjunction with Limma to do this? Also, I find the Bayesian theory in the paper by Gordon Smyth ("Linear Models and Empirical Bayes Methods..." tough

Bayesian Cancer limma bridge Bayesian Cancer limma bridge

updated 21.4 years ago • Richard Friedman

background correction with limma bg_minimum <- function(x){ return(list(norm = x$norm, bg = M_MIN__, agi = backgroundCorrect(x$agi, method = M_MIN__))) } #applies VSN...x$bg, agi = normalizeVSN(x$agi))) } #applies cyclic lowess normalization with limma nb_lowess <- function(x){ return(list(norm = M_LWS__, …

Annotation Normalization vsn limma Annotation Normalization vsn limma

updated 12.8 years ago • Cornish, Joseph NIH/NIAID [F]

of the last 28 years at the bench, I am finally getting my head round R programming. I've been using limma and affy to analyse a fairly chunky (and expensive!) Affymetrix hgu133plus2 data set and have been successful in generating...repository of data in hgu133plus2.db, there must be a way to tap into this without going 'outside' limma. Can anyone suggest how to do this? I'd be most grateful. Co…

GO hgu133plus2 affy limma convert GO hgu133plus2 affy limma convert

updated 14.9 years ago • David Iles

<div class="preformatted">Hello, I would like to know whether it is possible to analyze microarray data from a mixed model experiment with Limma package. I have 4 independent experiments (random effect) and 3 treatments (fixed effect), and 1 microarray (monocolor) for...like to know whether it is possible to analyze microarray data from a mixed model experiment with Limma package. I have 4…

Microarray limma Microarray limma

updated 16.3 years ago • Christian Brière

div class="preformatted">Dear Bioconductor members, I am using limma to analyze my microarrays. Therefore I apply lmFit and eBayes on my normalized data. Finally I write the result to a text

limma limma

updated 13.8 years ago • Pascal Gellert

Hello, I used limma to conduct a differential analysis. Everything worked fine but I can't seem to find something that explains what is...Hello, I used limma to conduct a differential analysis. Everything worked fine but I can't seem to find something that explains what is going...on behind the scenes. How does limma calculate the logFC? I have three replicates in my data and I applied li…

Limma Differential Expression Time-course Analysis

updated 6.6 years ago • mcfarn1

enter image description here][1] For paired data analysis using limma with multiple factor, if I was interested in the interaction effect between Condition and Time would the structure

DifferentialExpression limma

updated 2.5 years ago • Michael

<div class="preformatted">Dear list, I am analyzing a two color microarray dataset using limma. The dataset is from ArrayExpress database (accession number E-MEXP-1949). The samples include 4 mutants (rcd11, rcd13, rcd14...div class="preformatted">Dear list, I am analyzing a two color microarray dataset using limma. The dataset is from ArrayExpress database (accession number E-MEXP-194…

Microarray Normalization limma ArrayExpress Microarray Normalization limma ArrayExpress

updated 14.8 years ago • Yong Li

class="preformatted"> Hello all, I have a question about setting up blocks for paired samples in limma. In reading the user guide, limma book chapter, & mailing list, I have noticed most of the questions about paired samples

affy limma affy limma

updated 18.7 years ago • John Fowler

<div class="preformatted"> I'd like to suggest a merge function for MAlists be implemented in limma, since (I think) their are potential problems with the use of merge.RGlist and print-tip normalisation of the merged RG...<div class="preformatted"> I'd like to suggest a merge function for MAlists be implemented in limma, since (I think) their are potential problems with the use of mer…

Microarray limma Microarray limma

updated 21.9 years ago • Christopher Wilkinson

1.6">Hi all, How would you use the ballgown package in conjunction with voom, edgeR, DESeq, limma?</span> <span style="line-height:1.6">The bioarXiv paper seems to be making the claim that ballgown gaps the bridge between...cufflinks and tools like Limma, Voom, edgeR, DEseq.  </span> <span style="line-height:1.6">I don’t understand how voom, edgeR an…

limma rnaseq differential expression voom

updated 10.9 years ago • François Lefebvre

preformatted">Hi I am getting some rather confusing messages from the imageplot() function in limma. As in my previous mail, I am using a version of Bioconductor 1.2 from the website from about 2 weeks ago. I am reading the

limma limma

updated 22.4 years ago • michael watson IAH-C

div class="preformatted">Hi, I just stumbled onto an error creating contrasts in limma 2.12 on R 2.6.2, but could not find it in the mailing list archives or google, so I thought I might share it for the next person

limma limma

updated 17.8 years ago • Yannick Wurm

Hi Dears I am not very familiar with limma, I want use limma for finding DEGs of two different phenotype  But there are some ambiguous issues for me in using...limma for this work. Sample size of my phenotypes are completely different about 100 for control and 800 for case,now I don't...know does limma could be use for this work that have ___big ___and ___unbalanced ___sample …

limma microarray statistics

updated 9.6 years ago • tati6406

Dear Bioconductor users, I have been assuming that the base of the B-value log in Limma = 2, but I recently reread the paper and didn;t see a base. Is the base 2, and if not what is it/ Thanks and best wishes, Rich ------------------------------------------------------------ Richard

Cancer limma Cancer limma

updated 8.5 years ago • Richard Friedman

div class="preformatted">Hi, With limma, the moderated-t and its p-value provide a ranking guide because the various sorts of underlying assumptions are never

Microarray limma Microarray limma

updated 19.7 years ago • CHUNFA C JIE

Hi, I'm trying to use limma to get a list of differentially expressed genes between subtypes (GCB and ABC) of B-cell lymphoma. I have a dataset from...exprs(norm.batch) ``` But I'm just not sure where to start with creating a design matrix for the limma analysis

limma

updated 4.9 years ago • d808bc07

after having adjusted for differences between a normal and diseased tissue type (group ) using Limma rather than anova function in R, I have 2 questions - 1. Does Limma allow inclusion of covariates ? How do I first adjust the...a diseased sample and then understand the true difference between the exp of male and female in Limma. What I have been able to do uptil now is difference between males…

limma limma

updated 12.4 years ago • QAMRA Aditi GIS

there solution to offline running Bioconductor in R? For example I want to run Bioconductor package limma offline for that each time it ask for other dependency packages for which I need to download them from online site. Is

limma limma

updated 11.8 years ago • prabhakar ghorpade

<div class="preformatted">Hello, I have a data set of micro-array experiments (single color illumina) that is strongly confounded by pedigree relationships. I am just interested in comparing patients and controls. I would like to give Leek and Storey's sva algorithm a go with limma, to help deal with confounding factors. Does anybody have some experience doing this? My main concern is th…

GO limma sva GO limma sva

updated 17.5 years ago • Augusto Rendon

Dear Djie, I have generalized the removeBatchEffect() function so that it will now accept continuous covariates as well as batch factors. Just enter BSCE as the 'covariates' argument. The updated function will be on the devel version of limma, and I have attached it. Best wishes Gordon <pre> > Date: Tue, 31 Jan 2012 13:08:09 +0100 > From: Djie Tjwan Thung <djie.thun…

limma

updated 5.2 years ago • Gordon Smyth

<div class="preformatted"> I am working on some microarray data where the samples come from patients with different severities of disease state - something like "mild", "moderate", "severe". I suppose this is an 'ordinal' variable, but only know how to input categorical and continuous variables into the model and searching the Limma manual for the word 'ordinal' doesn't get me anywhere. I…

Microarray limma Microarray limma

updated 12.4 years ago • Guest User

To: bioconductor <bioconductor at="" stat.math.ethz.ch=""> > Subject: [BioC] Reading SMD data in limma > > Hello everyone ... i am trying to make an object from an SMD data > downloaded from ArrayExpress ... using the limma package

limma ArrayExpress limma ArrayExpress

updated 15.5 years ago • Gordon Smyth

I am getting unreasonably too small p-values from limma in my analysis. See the following minimal example in which a random variable has similar distributions in two conditions...So we expect to get an insignificant p-value. However, this is not the limma's output. n1 <- 100 topTable(eBayes(lmFit(c(1:n1, 1:n1), c(rep(0,n1),rep(1,n1)))), num=Inf, coef=1) The p-value in the outp…

limma

updated 6.1 years ago • Habil Zare

div class="preformatted">Hello, I have a curious problem involving Limma. I have an ExpressionSet object (called Seminoma) that contains the results of 18 samples (12 tumours and 6 normals). The...on probe "117_at" if I run a t-test() it produces a p-value of 0.1034 (no adjustment) whereas limma suggests it is 8.4e-07 (or 2.45e-06). My only thought is that something must be happening in th…

Cancer Biobase limma Cancer Biobase limma

updated 18.7 years ago • Daniel Brewer

may alter gene-expression profiles. In other words, an ANCOVA type tool. I am quite familiar with Limma (ANOVA) but including continuous variables is not very well described. Specifically, we have a project were two groups...and not in the other. Thus, we have implemented a longitudinal contrast with linear modeling through Limma. However, we are also interested in adding one or two continuous v…

RNASeq Microarray limma RNASeq Microarray limma

updated 12.2 years ago • Michael Breen

div class="preformatted">Dear all, I am using limma to perform differential analysis between two categories. Some samples in my set do not fall in either category. I can...1 0 GSM89747 1 0 GSM89739 0 1 GSM89687 1 0 GSM89708 0 1 After running limma on these sets, fit <- lmFit(SeminomaOnly,design2) cont.matrix <- makeContrasts(HvsL=High-Low, levels=design2…

Cancer limma Category Cancer limma Category

updated 18.4 years ago • Daniel Brewer

the differential gene expression between the normal and diseased tissues. I think I should use Limma Paired samples design matrix and compute paired moderated t test. Limma user guide. 9.4.1 pg no: 42 and 43.  Can anyone...td> <td>5</td> <td>DISEASED</td> </tr> </tbody> </table> My code  library(affy) library(limma) \# Read all C…

limma design matrix limma paired analysis limma

updated 8.3 years ago • anandprem1792

Dear all, about correcting the batch effects in **LIMMA and SVA,** 'd appreciate having your comments : assuming that we have a set of RNA-seq data (no treatment, + treatment) in many...Dear all, about correcting the batch effects in **LIMMA and SVA,** 'd appreciate having your comments : assuming that we have a set of RNA-seq data (no treatment, + treatment) in many distinct...BA…

limma combat sva

updated 6.5 years ago • Bogdan

sig.probe2<-probe2[which(probe2$adj.P.Val<=0.05),] write.table(sig.probe2,file="limma..model2.significant..output.txt",sep="\t",quote=TRUE) write.table(probe2,file="limma..model2..output.txt",sep="\t",quote=TRUE...sig.probe3<-probe3[which(probe3$adj.P.Val<=0.05),] write.table(sig.probe3,file="limma..model3.significant..output.txt",sep="\t",quote=T…

Regression limma STATISITICS HPC

updated 21 months ago • Jitendra

sample was used to hybridize on Green channel. This is a paired design and a reference design. Limma manual describes examples unique to one specific design. I do not know how to combine two different designs. My targets

Microarray Cancer limma Microarray Cancer limma

updated 17.1 years ago • Adrian Johnson

div class="preformatted">Dear All, I'am using limma package to extract the genes diffrentially expressed by 3 treatment,my database includes 48803 genes (rows) and 120

limma limma

updated 16.8 years ago • Mohamed lajnef

Hi, I was wondering if its possible to incorporate technical reps and biological reps in Limma. There was a post some time ago saying this would be implemented, is it possible in the current version? We have 6-7 biological

limma limma

updated 21.9 years ago • Simon Melov

enter image description here][1]Hello, I am attempting to remove batch effects from my data using `limma::removeBatchEffect()`. I have two batches of samples, and there are four conditions. In the figures below batches are color...coded. I'm wondering why the batch effect seems stronger after applying the `limma::removeBatchEffect()`. The functions were running with default parameters, as f…

limma deseq2

updated 6.5 years ago • lech.kaczmarczyk

div class="preformatted">Hi BioC, I have question about LIMMA makeContrasts( ) function. I am reading parameter file for LIMMA from out side R environment and building design matrix

limma limma

updated 21.0 years ago • Saurin D. Jani

Hi all, I use limma to compare pathway score between 3 groups. Then I would like to make boxplot with overall p value and pairwise p value...significance-levels-to-ggplots/ The value from t test or anova is different from the p value from limma: topTable <- topTable(fit2, number=Inf, sort.by="none") topTableLSvsNC <- topTable(fit2, coef="LSvsNC", number=Inf, sort.by...for…

t.test boxplot limma anova

updated 21 months ago • Chris

div class="preformatted">Does anyone have experience using limma with 2-color microarray data obtained from the Applied Precision SoftWorx Tracker? I can read the .txt files with read.maimages

Microarray limma Microarray limma

updated 20.2 years ago • Susan J. Miller

div class="preformatted">Hello, I have used Limma for preprocessing and statistical analysis. I want to filter my gene list after the statistical analysis but before

Preprocessing limma Preprocessing limma

updated 16.9 years ago • Sally

available from GSEA (C1,C2,C3 and C4) into a 4 different gene sets, so that I can use geneSetTest of limma on above 4 different gene sets. In one of the examples (classic estrogen example, only one set is described). What kind of

limma convert limma convert

updated 17.6 years ago • Srinivas Iyyer

div class="preformatted">Hi dear all, I am using limma for two color Agilent Microarray analysis. I found that normalizeBetweenArrays does not perform Quantile normalization...this way it is correct or not and why M values are not normalized directly while it is mentioned in limma user guide that quantile method normalize M values. This question was raised earlier in Bioconductor list ( htt…

Microarray limma Microarray limma

updated 12.3 years ago • neeraj rana