Bioconductor Forum

preformatted">I have a 2 x 3 factorial cDNA microarray experiment which I would like to analyse in Limma. I need, however, some advise on the constuction of design and contrast matrices - which is not straightforward to understand

Microarray GO limma Microarray GO limma

updated 21.8 years ago • Per Gregersen

div class="preformatted">Hi list, I am trying to call makeContrasts() in limma to accept character vector of all samples vs control. But it seems that makeContrasts() consider only the first element

limma ASSIGN limma ASSIGN

updated 18.2 years ago • Amin Moghaddasi

I noticed that there is inconsistency between the t and p.value on the topTable output using Limma package to analyze a dye swap two channel array experiment. logFC AveExpr t P.Value adj.P.Val B 1401 3.216254 11.74137

limma limma

updated 16.3 years ago • Julie Zhu

<div class="preformatted">Hi everybody, The human Agilent chip 4x44 has most of the probes only once, but some of then appear in 10 replicates. These replicates are genes and not controls. I am using the Limma package to analyze them. I would like to define these replicates as technical ones and leave the other probes (those that...some of then appear in 10 replicates. These replicates are…

limma limma

updated 18.5 years ago • Ester Feldmesser

div class="preformatted">Hi There, I am using normalizeWithinArrays function from the limma package for a within array normalization . There were no missing/NA values in the input data file, however, after the within

aCGH Normalization limma aCGH aCGH Normalization limma aCGH

updated 13.4 years ago • Zhang, Xueqiong

Hi I use limma to find DEGs between chemo-resistance and chemo-sensitive samples, in limma output I found that e.g one of my genes has

limma microarray DEG

updated 9.1 years ago • Shamim Sarhadi

Hi, limma function fitFDist() has a bug, triggered under rare circumstances.  As per the documentation: _fitFDist(x, df1, covariate...Platform: x86\_64-redhat-linux-gnu (64-bit) Running under: Fedora 25 (Workstation Edition) \[1\] limma\_3.30.7     betr\_1.33.0 Thanks ! --c &nbsp

software error limma

updated 9.0 years ago • Rifius

div class="preformatted">Hi, I am relatively new to Limma. I want to filter my gene list after my statistical analysis. What object do I filter on (fit2?)? I looked at genefilter and...filter on the ExpressionSet. But this occurs before the statistical analysis. Sally Here is my Limma script: #Load libraries source("http://bioconductor.org/biocLite.R") biocLite() library(limma) library(…

genefilter multtest limma genefilter multtest limma

updated 16.9 years ago • Sally

<div class="preformatted">Dear Ryan, The limma algorithm is very well understood by now, and there are many bioinformatications at the FHCRC who could probably answer your question. I find it hard to make a response to your email because I just see a jumble of numbers. I don't have a firm understanding of what your experimental design is, what model you've fitted, what the numbers are th…

Cancer limma Cancer limma

updated 13.1 years ago • Gordon Smyth

I am having a query related to VOOM function in the limma package. I am trying to analyze proteomics data using limma to identify the differential expression between two groups...and not any technical ones. I have a doubt that the matrix design is correct or not . Also limma can be used for the analysis  proteomics data obtained from masspectrometry platform . design <- model.mat…

limma

updated 7.2 years ago • manubhaikp

div class="preformatted">I have a 2x2 factorial design which I ran through limma. The factors are (1) species [(Coho (c)) and Sockeye (s))] and (2) sample time (0, 24, 48 and 96 hours). The R script used was: source("http://bioconductor.org...biocLite.R") library(limma) library(Biobase) exprdata<-read.table("exprsData.txt", header=TRUE,sep="\t",row.names=1,as.is=TRUE,fill=TRUE,) …

limma limma

updated 17.8 years ago • Sally

class="preformatted">Hi, I'm trying to do an analysis of some tag3 Affy microarray data with the limma package, and I've run into a problem I'm not sure how to solve. The data comes from a series of arrays recorded at different...basis. Hopefully this will improve the quality of the linear regression. So, is there any trick in limma (or in the preprocessing step prior to limma) for combinin…

Microarray Preprocessing Regression Yeast probe affy limma Microarray Preprocessing Yeast

updated 17.2 years ago • Alex Gutteridge

Dear limma experts, I am running a limma analysis where I am testing for differential expression analysis and I have two variables...ATPostVsPre = AT_post - AT_pre, levels = colnames(design_matrix) ) fit_1 <- limma::eBayes( limma::lmFit( data_matrix, design_matrix ) ) ebayes_fit <- limma::eBayes( limma::contrasts.fit( fit_1…

limmaGUI lim MultipleComparison multip

updated 22 months ago • roger.moreno.justicia

0+Group) when you needed design <- model.matrix(~Group) However, I do not recommend a limma analysis of RPKM values, because it does not respect the mean-variance relationship inherent in the count data. Nicole...analysis RNA-Seq data has moved on considerably since then. Please see the last case study in the limma User's Guide, which analyses the Nigerian HapMap data, for how I rec…

HapMap limma HapMap limma

updated 14.1 years ago • Gordon Smyth

Hi, I've been using the differential splicing functions within limma as outlined in the user guide. I've updated to the newest version of limma today and it looks like the functions topSplice...have now been removed from the package (within diffSplice.R)  <pre> > library(limma) > topSplice() Error in topSplice() : could not find function "topSplice" &g…

limma

updated 8.2 years ago • gmuir

is in Log2 RUV-normalized expression. I want to perform differential expression analysis. Is the limma package in R fit for this? From what I've read the limma package expects Log2 expression data without normalization, but

RUVnormalizeData MicroarrayData limma

updated 2.6 years ago • pg45863

div class="preformatted">Hi everyone, I am using the function genas from the Limma package to calculate the logFC correlation between some contrasts. genas(fit.contrast, coef = c(2,3), chooseMethod = "Fpval

limma limma

updated 12.2 years ago • Christian De Santis

div class="preformatted">Dear Gordon et al. I've just noticed an oddity in the way how limma's contrasts.fit function handles missing observations, and I wonder if it might be a bug. Please have a look at the following...lmFit, I unsurprisingly get a warning that some coefficients cannot be estimated: > library( limma ) > fit <- lmFit( y, dm ) Warning messag…

limma limma

updated 16.8 years ago • Simon Anders

<div class="preformatted">Dear Guido, Thanks for the reminder. A bug fix for genas() has been included in limma 3.18.4, so that genas() now handles vector df.prior in a graceful manner. Best wishes Gordon > Date: Wed, 27 Nov 2013 14:30:08 +0000 > From: "Hooiveld, Guido" <guido.hooiveld at="" wur.nl=""> > To: "bioconductor at r-project.org" <bioconductor at=…

limma limma

updated 12.1 years ago • Gordon Smyth

<div class="preformatted">Dear Peter, I have thought from time to time about adding single-channel capability to limma and read.maimages(). I haven't done it so far because I don't see this sort of data in my own work, so I have been unsure of the special needs here, and also undecided about the data class to read into. I guess it will happen when it is clear in my mind what needs to be …

probe limma probe limma

updated 18.6 years ago • Gordon Smyth

<div class="preformatted"> I would like to find the differentially expressed genes for several variables using the limma package for several groups. -- output of sessionInfo(): I have the rma normalized matrix in the following format : ID_REF GSM362180 GSM362181 GSM362188 GSM362189 GSM362192 244901 5.094871713 4.626623079 4.554272515 4.748604391 4.759221647 244902 5.194528083 4.…

limma limma

updated 13.2 years ago • Guest User

a > targets dataframe, why not use it as an argument to read.maimages() as > shown in > the limma user's guide? > > Guess #2, the 8x60K data files I have for testing do not contain a column > "GeneName" > which is probably...gt; Date: > 07.03.2011 16:23 > Subject: > [BioC] Problem with read.maimages (Limma): Error in dimnames(x…

Annotation GO limma Annotation GO limma

updated 14.8 years ago • Hari Easwaran

Bulashevska <s.bulashevska at="" dkfz-heidelberg.de=""> >Subject: [BioC] a problem with package limma (read.maimages) >To: bioconductor at stat.math.ethz.ch >Message-ID: <4492A215.5070105 at dkfz.de> >Content

limma limma

updated 19.6 years ago • Gordon Smyth

with both microarray and RNA-Seq data. For differential expression analysis of microarrays, I used `limma` with log2 transformed intensities as input. For RNA-Seq, I used `DESeq2` with raw counts (derived from `salmon`) as input. Why...does `limma` want/require log2 transformed intensities but `DESeq2` wants untransformed counts? I'm aware that `limma` uses a different...heteroscedasticity …

limma DifferentialExpression DESeq2

updated 4.6 years ago • tjbencomo

Given a matrix of limma voom normalized genes, I want to do Survival Analysis of a particular gene X. The design matrix applied on voom was achieved...How should I convert this matrix into this nominal shape? Possibilities: 1. I understand that limma voom results in negative, neutral (near to 0) and positive, so negative means underexpressed, near to zero normal and positive

RNASeqData limma voom PFS DGE

updated 2.5 years ago • manuelsokolov

Hello, I have been working on microarrays using R and Limma for differential gene expression analysis. My current design is fairly simple as I am just using two class "control...Hello, I have been working on microarrays using R and Limma for differential gene expression analysis. My current design is fairly simple as I am just using two class "control" and...almost all DE genes are the same but…

limma design matrix

updated 8.9 years ago • Stane

Hi all, I am developing an analysis of protein microarray data and have found that limma performs very well in terms of identifying positive controls in the assay. Unfortunately, there are a large number...Hi all, I am developing an analysis of protein microarray data and have found that limma performs very well in terms of identifying positive controls in the assay. Unfortunately, there are a …

limma nonspecific filtering weight

updated 7.4 years ago • andrew.birnberg

Hi, I am learning how to use limma for bulk RNA-seq data. Below is a snapshot of the metadata file. ![enter image description here][1] My samples are categorised...Hi, I am learning how to use limma for bulk RNA-seq data. Below is a snapshot of the metadata file. ![enter image description here][1] My samples are categorised by Sex (Male and Female) and by 6 Age categories (Infan…

limma R

updated 4.5 years ago • lintek08

2006 07:29:07 -0700 (PDT) >From: Alfredo Juncal <alfjuncal at="" yahoo.com=""> >Subject: [BioC] Limma weights, P values and differential expression >To: bioconductor at stat.math.ethz.ch > >Dear Limma users, > &gt...I > still do not fully understandf how weights are used when applying > the linear model. In limma, weights are alw…

Normalization Bayesian Regression probe limma Normalization Bayesian Regression probe

updated 19.4 years ago • Gordon Smyth

gt;From: "michael watson (IAH-C)" <michael.watson@bbsrc.ac.uk> >Subject: [BioC] Confusion over limma documentation and design/contrast >To: "Gordon Smyth" <smyth@wehi.edu.au> >Cc: bioconductor@stat.math.ethz.ch &gt...multiples the vector of regression coefficients. Whenever the word "coefficients" is used in the limma documentation, it refers to the regression…

GO Regression limma GO Regression limma

updated 21.1 years ago • Gordon Smyth

at="" gmail.com=""> > Subject: [BioC] extremely low adjusted p-values in regression using > limma > To: "Bioconductor List" <bioconductor at="" stat.math.ethz.ch=""> > > Dear all, > > I am trying to run a regression analysis...on my microarray data using the > limma and all the genes are showing adjusted p-values lower than 10…

Microarray Regression limma Microarray Regression limma

updated 17.8 years ago • Gordon Smyth

Dear Bioconductors Friends! I did a parametrization, based on 8.7 Factorial Designs section on limma usersguide, in a 2x2x2x4 factorial experiment and I would like to ask you if I did a correct script for limma. Here is my

limma limma

updated 17.8 years ago • Marcelo Laia

<div class="preformatted">Hello, I'm using Limma to assess differential expression on double colour microarray data and have a question about the lmFit function. When...div class="preformatted">Hello, I'm using Limma to assess differential expression on double colour microarray data and have a question about the lmFit function...vs treated) in a classical design experiment "Two Groups: C…

limma limma

updated 16.4 years ago • Benoit

Hello, I have multi level experiment limma design. I want to ask after I create fit object by `` fit <- lmFit(v,design,block=targets$Subject,correlation=corfit

limma

updated 9.5 years ago • zzjerryzhang

Dear all, I am running limma's _decideTests_ on DNA-methylation "M" values, which range from -6 to +6. The fact that some values are __negative__ leads

limma decidetests methylation

updated 9.8 years ago • kraiczy

Symbols s1 s2 g1 2.3 4.5 g1 4.5 2.3 I have used limma::avereps to get unique gene symbols, however, i got unique gene symbols but the expression values was not averaged. The

limma

updated 5.0 years ago • lily

is a cutoff then B=log odds>0 is the cutoff. According to Gordon Smyth the author of Limma (and Gordon please correct me if I am wrong) the B>0 cutoff is recommended over p-value cutoffs. If you wish to use a p-value...my question > is when i obtain the list list of p-value of different genes > (after executing limma) > i don't know if i consdier all …

limma limma

updated 18.5 years ago • Richard Friedman

I have a dataset from non-genomic data. 150 compounds was measured in leaves after a insect contact and non-insect contact (control). I have leaves in resistant and susceptible genotype. A subset of my data can be found at [here][1]. Supposing Compound (Composto vary from 1 to 150) are genes, I used limma to get "differential" compunds between Genotypes, Estado (Resistante or Suscptible) and …

non-genomic quantitative limma

updated 4.6 years ago • Marcelo Laia

how I'd go about doing this with >>>> > > Bioconductor? Is it possible using the Limma package? Is there any >>>> > > code out there to assist me? >>>> > > >>>> > > I've experience in analyzing...Affymetrix data using Limma and …

miRNA Microarray Normalization GO limma miRNA Microarray Normalization GO limma

updated 17.6 years ago • Gordon Smyth

15.39, Johan Lindberg wrote: >> >>> Dear all. >>> >>> I have used Limma to analyse my data and I got no differentially >>> expressed genes correcting with multiple testing using fdr...an fdr < 0.05. >>> >>> I immediately thought I had done something wr…

limma limma

updated 17.5 years ago • Johan Lindberg

if anyone here knows something about the software, and if this > software has more function than limma. > > Thank you very much! > -- > Xiaopeng ZHANG<xpzhang@genetics.ac.cn> > > _______________________________________________

Genetics limma GeneSpring Genetics limma GeneSpring

updated 21.1 years ago • donghu@itsa.ucsf.edu

Dear Community, I have a question about the voom-limma of RNA-Seq data analysis. I have multi-factor design with three factors: A (16 levels), B (2 levels) and C (three levels), and A is...Dear Community, I have a question about the voom-limma of RNA-Seq data analysis. I have multi-factor design with three factors: A (16 levels), B (2 levels) and C (three levels), and A is the random effect. M…

limma

updated 9.3 years ago • Yanzhu Lin

<div class="preformatted">Dear Limma users, In our lab we print our own microarray slides. We print both dedicated and whole genome arrays. With dedicated arrays...div class="preformatted">Dear Limma users, In our lab we print our own microarray slides. We print both dedicated and whole genome arrays. With dedicated...If have written a "little" function and extension for the normalizat…

Microarray Normalization limma Microarray Normalization limma

updated 21.1 years ago • Breuk102

2007 11:17:06 +0100 (BST) >From: Misha Kapushesky <ostolop at="" ebi.ac.uk=""> >Subject: [BioC] Limma - small bug in decideTests? >To: bioconductor at stat.math.ethz.ch >Message-ID: <pine.lnx.4.64.0706171104290.17169...has started to publish in the past year on hierarchical tests, but nothing yet which applies to the limma situation. So the method="hierarchica…

limma limma

updated 18.5 years ago • Gordon Smyth

div class="preformatted"> I use limma quite a bit but have not really been using arrayWeights much, until recently. I like it a lot but have found, in some cases...to access array quality and produce weights , that this will then naturally bias a method such as limma that then using a linear model, again, to determine differential expression. After trying a few different permutations

Clustering limma Clustering limma

updated 17.5 years ago • Paul Leo

div class="preformatted">Hello, I am using limma package to read my data into R, and I use the following command to read gal file to get layout, however, I got the following

limma limma

updated 21.8 years ago • Joyce Gu

<div class="preformatted"> Hi all, I am trying to reproduce the results I get with contrasts.fit function in limma using simple math, but it does not work when the contrast is made of more than two groups. Here is the code I am using. Any suggestions...preformatted"> Hi all, I am trying to reproduce the results I get with contrasts.fit function in limma using simple math, but it does n…

limma limma

updated 17.3 years ago • Tarca, Adi

div class="preformatted">Hello, I'm trying to analyze a set of Combimatrix arrays with LIMMA and have a couple of questions. I haven't found anything on this list about Combimatrix arrays, so I might just start by

limma limma

updated 17.3 years ago • Paul Harrison

i am trying to make an object from an SMD data downloaded from ArrayExpress ... using the limma package and used the following command .... but getting this error and the object is not being created .. data <- read.maimages

limma ArrayExpress limma ArrayExpress

updated 15.6 years ago • Rohit Farmer

Hi my understanding is that we should not use corrected counts with something like edgeR or limma? **However, because ComBat_seq is correcting at the raw count level** and then input into edgeR for TMM follow with voom...Hi my understanding is that we should not use corrected counts with something like edgeR or limma? **However, because ComBat_seq is correcting at the raw count level** …

sva limma

updated 4.4 years ago • Ahdee

<div class="preformatted">Dear Eduardo, I understand that "method" relates to how contrasts are compared. There is a description in these posts: https://stat.ethz.ch/pipermail/bioconductor/2008-January/020646.html https://mailman.stat.ethz.ch/pipermail/bioconductor/2012-May/045488.ht ml You will see that "separate" method in decideTests will give the same result as topTable. This is a ve…

Microarray limma Microarray limma

updated 13.5 years ago • Mark Cruickshank

Dear all, I am performing a very simple limma voom analysis on 2 groups, but I am getting different results when I use make.contrasts() and when I don't. The aim is simply...to find differentially expressed genes between 2 groups. I have read the limma voom guide and edgeR guide but they seem to give different examples (using make.contrasts and not, which gives me different

contrasts limma voom

updated 3.8 years ago • S T

Hello, I am performing a differential analysis with limma, I have three groups: a control group, and two disease groups (D1 and D2), and I want to perform two contrasts, D1- CTRL and D2...Hello, I am performing a differential analysis with limma, I have three groups: a control group, and two disease groups (D1 and D2), and I want to perform two contrasts, D1- CTRL and D2-CTRL whilst blocking fo…

limma

updated 9.3 years ago • obarton

where time cannot be consider as a continuous variable), 2 rep each.  I have imported them with limma and </span>normalized<span style="line-height:1.6"> with vsn </span>normalization<span style="line-height:1.6...in order to perform clustering after.</span> From the vignette I understood that the F-test of limma would give me what I…

limma F-test

updated 10.8 years ago • samuel collombet

I am new to limma so please excuse my ignorance. I am trying to use limma-voom to compare the effect of a treatment between males and females

limma limma design matrix limma contrast matrix limma paired analysis limma-voom

updated 8.9 years ago • gregory.l.stone

<div class="preformatted">At 02:48 AM 18/03/2004, Jordi Altirriba Guti?rrez wrote: >Thank you very much Gordon for your quick answer! >My phenoData is: >>pData(eset) > DIABETES TREATMENT >DNT1 TRUE FALSE >DNT2 TRUE FALSE >DNT3 TRUE FALSE >DT1 TRUE TRUE >DT2 TRUE TR…

GO limma factDesign GO limma factDesign

updated 21.8 years ago • Gordon Smyth

But in fact, they can be estimated just using data from other 9 patients.? Is there a way to tell limma to do that? Thanks! Tao library(limma) dat <- matrix(rnorm(400), ncol=40) ptID <- factor(rep(1:10, each=4)) day <- factor(rep(1:4,10)) dat

limma limma

updated 12.6 years ago • Shi, Tao

div class="preformatted">Hi, I have been analyse a time course experiment with limma and I get the end of section 16 in userguide very well. But, I don't know how do I do to get the names of genes differentially

limma limma

updated 20.9 years ago • Marcelo Luiz de Laia

I have been analysing protein array data with hundreds and thousands of proteins using Limma in R. For normalisation I have been using the following: y <- normalizeBetweenArrays(log2(exprs), method="quantile") followed...plots and density plots for QC. Followed by model fitting for differential expression analysis in Limma. However we then chose the most promising 35 prote…

limma microarray r

updated 7.0 years ago • reubenmcgregor88

Hello, I am using limma to determine differential gene expression between healthy and KO mice. In my design matrix, I am including several...Hello, I am using limma to determine differential gene expression between healthy and KO mice. In my design matrix, I am including several covariates that I know influence gene expression, but that I am not interested in. Specifically, it looks s…

limma DifferentialExpression

updated 3.9 years ago • nhaus