Bioconductor Forum

Are repeated measures anova with limma(IE using duplicate correlation and a blocking variable and a measurement covariate) directional?  Will it automatically

limma

updated 11.0 years ago • kodream

Hello there, My mouse array data and human array data were derived from the same two conditions, condition A and condition B. I fitted two array data individually using limma and the fitted expression values were obtained using the as.matrix(y). Now my question is: may I directly compare the mouse...the same two conditions, condition A and condition B. I fitted two array data individually usin…

limma

updated 6.6 years ago • capricygcapricyg

<div class="preformatted">James W. MacDonald <jmacdon ...="" at=""> writes: > > Hi J.M., > > On 2/13/2012 9:35 AM, J.M.Jensen [guest] wrote: > > Dear all, > > I am trying to create a customized cut flow with the affy/limma packages. In order to assign different > cut-off values between different arrays would be to first m…

GO limma ASSIGN GO limma ASSIGN

updated 13.9 years ago • J.M.Jensen

Hi, I'm trying to use `limma`'s `voom` for RNA-seq data, where my design matrix contains `NA` values. Can `voom` handle these `NA`s or is the only solution to...Hi, I'm trying to use `limma`'s `voom` for RNA-seq data, where my design matrix contains `NA` values. Can `voom` handle these `NA`s or is the only solution to toss...dge <- edgeR::DGEList(counts = counts.mat) dge <- e…

limma voom design NAs

updated 3.6 years ago • dr

Hello, Referring the limma user guide section 9.7-Multi-level experiments (pages 49-50), This experiment involves 6 subjects, including 3 patients...Diseased, Normal Tissue type: A, B https://www.bioconductor.org/packages/devel/bioc/vignettes/limma/inst/doc/usersguide.pdf I understood that you can test for Diseased vs Normal for TissueA or Diseased vs Normal for

limma microarray affy

updated 6.1 years ago • cyusufd

large changes in differential expression I wanted to use the cyclic loess normalisation within limma rather than quantile normalisation. I used the default settings i.e. y<-normalizeBetweenArrays(x,method="cyclicloess

limma limma

updated 13.2 years ago • Guest User

differences. I would like to export either normalised_counts (OR) vst or rlog, and import it to `limma` for differential expression using `limma-trend`. Can we use rlog or vst data values in limma for differential expression

DESeq2 limma Normalization R

updated 3.1 years ago • Sabiha

beside the plot to show what each colour stands for, but "legend" is not included as an argument of limma's volcanoplot

limma

updated 9.7 years ago • christopher.clarskon15

div class="preformatted">Dear List, I have a problem of estimability using LIMMA that I do not know how to solve. I think that I am using the right model, but I can not solve the problem so I need someone to...12 6 ko t It is exactly the same as the example 8.3 in the limma user guide, except that I have two strains, WT and KO with the same paired stru…

GO hgu95av2 Ruuid multtest affy graph limma RBGL qvalue Category affyio GO hgu95av2

updated 19.6 years ago • Pedro López Romero

including an effect for probe-specific dye effects in the design matrix. See page 57 of the limma User's Guide (section on dye swaps). Best wishes Gordon > Date: Mon, 26 Aug 2013 04:43:20 -0700 (PDT) > From: "Jana [guest]" <guest at...gt; To: bioconductor at r-project.org, jana.asselman at ugent.be > Subject: [BioC] Complex Limma design: technical replication, > …

Microarray limma Microarray limma

updated 12.4 years ago • Gordon Smyth

I have additionally a grouping where each sample belongs to one of E,F,G. I would like to use Limma to find out statistically significant bacteria between E,F,G without having to do pairwise-comparisons (EF,EG,FG). That...is, much like anova results are interpreted. For some reason I have found only Limma contrast matrix examples for pairwise-comparisons. &nbsp

limma

updated 9.6 years ago • sami.pietila

<div class="preformatted">Hi Gordon Thanks for the response. I worked through my two examples and found out they are equivalent. >Do you know how to multiply a vector by a matrix? If you do, then I think >the best way to figure out what the design matrix is doing for you is just >to sit down with a piece of paper and a pencil for a few minutes, and >multiply t…

Microarray GO limma Microarray GO limma

updated 21.2 years ago • michael watson IAH-C

to respond to a number of questions about the interpretation of the moderated t and B-statistics in limma. This will be a section of the Limma User's Guide in the next release. Gordon ---------------------------------- __Statistics for Differential Expression__...provides several methods to do this (see the Section "Multiple Testing Across Contrasts" in the limma User's Guide

Microarray limma

updated 5.2 years ago • Gordon Smyth

Hello everyone ! I wanted to ask a particular question regarding the implementation of limma R package, for DE regarding proteomics multiplex immunoassay technologies. In particular, my experiment is related...normalized)-log2 transformed-log2 & median centered data][1] For differential expression with limma, and based on my above description, even the log2 transformation could suffice? …

DEanalysis limma olinktargetedproteomics

updated 10 months ago • svlachavas

Hello: <span style="line-height:1.6">I performed some limma analysis using simulated data. For each gene, I fitted a “plain” linear model (lm() in R), limma with no trend, limma with trend

limma edgeR

updated 10.2 years ago • Nik Tuzov

the average but I am just not aware of >that. I have used the duplicateCorrelation() function in Limma which gives >me a -0.04 correlation and its probably because the probes are position >randomized (even the duplicates...design) > >-------------------------------- >function: duplicateCorrelation() in limma as follows: > >biolrep=c(1,1,2,2)…

Normalization limma Normalization limma

updated 16.7 years ago • Jenny Drnevich

with an appropriate design matrix, while including covariates like age and sex, and then how to use limma for testing associations between pathway activities and the continuous disease progression metric. There are about...arrange(P.Value) ``` - Is this the appropriate way to model continuous relationships in limma? I'm particularly uncertain about using eBayes() with a continuous predicto…

limma DifferentialExpression Designmatrix

updated 12 months ago • Tadeoye

<div class="preformatted"> Hi list, I have a one-color setup with 238 samples and 6 conditions, for a geneset of just over 400 probes (targeted array). One of the conditions is control and the rest are experimental conditions. After normalization using vsn I would like to make a comparison first between the control and the rest and then between some of the conditions grouped. Being human s…

vsn limma vsn limma

updated 15.0 years ago • David A.

<div class="preformatted"> Hi so I'm trying to do limma fitting on my data but i keep getting the following error Error in rowMeans(y$exprs, na.rm=TRUE):'x' must be numeric But I'm...div class="preformatted"> Hi so I'm trying to do limma fitting on my data but i keep getting the following error Error in rowMeans(y$exprs, na.rm=TRUE):'x' must be numeric But I

limma limma

updated 13.3 years ago • Kripa R

I have 4 experimental conditions (4 genotypes), with 3 sample for each one, which I'm using limma for the differential expression analysis. If I follow the limma guide and keep exons that have more than 1 cpm in

voom limma rna-seq differential gene expression

updated 9.4 years ago • rubi

I want to get the difference of differences from a limma voom analysis. In a simplified example, I have 3 genotypes: Parent1, Parent2 and the Hybrid (of the two parents). For this...I want to get the difference of differences from a limma voom analysis. In a simplified example, I have 3 genotypes: Parent1, Parent2 and the Hybrid (of the two parents). For this example

limma DifferentialExpression

updated 2.7 years ago • mpitz

biological replicates and A and B always come with Cy5 in each clip. I used the following codes in Limma. Design<-cbind (A=c(1,1,1,1,1,1,0,0,0,0,0,0), B=c(0,0,0,0,0,0,1,1,1,1,11)) fit1<-lmFit(MA, design) Then I got two coefficients, the first one is

multtest limma multtest limma

updated 21.8 years ago • rwin qian

div class="preformatted">Hello, I have a question about nested design and model.matrix in limma (one channel arrays). In this design, each value of variable "source" is nested in (found in combination with only one value

limma limma

updated 15.6 years ago • F F

supplement and exercise effect? 4) Sex effect ? So to do so, I need to run paired analysis in limma, but till now the design does not work properly. May I ask you to give me some help how to design as I should consider several

limma limma

updated 12.5 years ago • Fazelzadeh, Parastoo

div class="preformatted"> Hello all I want to load imagene data with limma and have encountered problems I have used the following command to read the data, and get an error: > RG <- read.imagene

Genetics limma Genetics limma

updated 16.6 years ago • Ingunn Berget

<div class="preformatted">Dear All, While looking at the Limma user guide, I came across the following example > targets <- readTargets("SwirlSample.txt") > RG <- read.maimages(targets...div class="preformatted">Dear All, While looking at the Limma user guide, I came across the following example > targets <- readTargets("SwirlSample.txt") &…

limma limma

updated 20.7 years ago • Ankit Pal

I am using limma to identify proteins that are differentially expressed in a tissue collected from four subjects at two different...for repeated sampling from the same individual. I tried 1) blocking by subject (p. 43-44 of limma manual) and 2) computing within-subject correlation and including it in the model (p. 111 of limma manual). The consensus

limma repeated measurements blocking random effects

updated 5.8 years ago • jkhudyakov

div class="preformatted"> Can someone please explain the example given in the limma vignette on page 45. It is an example of the classic interaction model. There are two different scenarios that are shown

limma limma

updated 12.8 years ago • Guest User

class="preformatted">Hallo to everyone, In have a model like the factorial design example in the limma user guide TS <- factor(TS, levels = c("WT.U", "WT.S", "Mu.U", "Mu.S")) design <- model.matrix(~0 + TS) colnames(design) <- levels(TS) cont.matrix

limma limma

updated 15.3 years ago • MassimoAcquaviva@ospedale-gaslini.ge.it

div class="preformatted"> Dear All, Now I'm using limma to do microarray analysis. In limma User's Guide (ver. 22 October 2008), Chapter 9, there is only one case for "Separate Channel

Microarray limma Microarray limma

updated 17.0 years ago • Kun Zhang

Hi, I am analyzing an RNA seq experiments using limma in which I have 4 different RNA species A,B,C,D and each has three replicates.  I am using the follwing (assuming data

limma multiple factor design

updated 10.5 years ago • ea1402

During the p.adj , many measurements (different genes) from the same sample (i.e one column of the image) does it take all the p values from across all the samples and rank them? or ranking gene by gene and calculate the p.adj? For example, if we have 100 genes that we want to test for differences between three samples A, B and C, then do we generate 100 p-values for A x B, 100 p-values for…

limma r transcriptomics FDR statistics

updated 6.3 years ago • Wuschel

class="preformatted">Hi, I've got some 0-weight features on my arrays that are leading to NAs in limma where the log ratio cannot be estimated. Strangely to me, this also happens when I do differential expressions between...graphics" "grDevices" "utils" "datasets" [6] "methods" "base" other attached packages: limma "2.10.4" Francois </div

GO GO

updated 18.6 years ago • Francois Pepin

I was surprised that limma sometimes returns very small p-values in comparisons where one group is completely missing. And I am sorry if this is...I was surprised that limma sometimes returns very small p-values in comparisons where one group is completely missing. And I am sorry if this is already a well-known behavior, I tried to search for descriptions of this, but couldn't find anything that …

limma

updated 2.8 years ago • Constantin Ahlmann-Eltze

Dear All, How would you model a factor that's heteroscedastic using limma-voom for RNA-Seq data? Best, Yanzhu

limma

updated 9.2 years ago • Yanzhu Lin

2 biological replicates and 2 conditions, before and after stress. I have used the ratio number in limma and got reasonable results. Meanwhile, I also get suggestions to use edgeR with summed poly-counts as input and total...step. Any suggestions and thoughts with my codes? I am also wondering what people think about using limma vs. edgeR for this analysis. Thanks, Elisha

edgeR limma offset

updated 7.7 years ago • catpaw.tw

Firstly i downloaded data from GEO then i compress and unzip it (for eg:GSE14325) i have 9 GSE ids fro my work. __Data preprocessing and Identification of DEGs :(i am following this step)__ The raw expression datasets were downloaded and preprocessed by log2 transformation in R language . The Linear Models \`\`limma'' package in R language wasused to analyze the microarray datasets . Differenti…

RMA normalization

updated 8.8 years ago • nia

div class="preformatted">Hi, I am using the current version of LIMMA (January 25, 2009) and am having the following error message from this script below: Error Message: Error in new("AnnotatedDataFrame...Problematic Script (Note this script was originally run successfully under the version of LIMMA current during the winter/spring of 2008, but is not working now): > setClass("Annotat…

limma limma

updated 16.9 years ago • Sally

in the graph? I used the argument `xlab` and `ylab` options, but did not see the name I wanted limma::plotDensities.default(object = exp, xlab = "sample", ylab = "expression") This method just returns the density and intensity

desnity limma

updated 3.8 years ago • adR

I have noticed that limma's volcanoplot() function uses uncorrected p-values from the MArrayLM objected. My question is: why? I've seen an old

volcanoplot limma fdr

updated 5.1 years ago • tcalvo

Hi there, I'd like some guidance on how best to carry out differential expression analysis using the limma pipeline with my data set. Below is representative of my targets data.frame: Sample Patient Tissue Time Treatment Class 1 1 Diseased 0 Topical A 2 1 Diseased 2 Topical A 3 1 Diseased 4 Topical A…

limma rnaseq r

updated 5.7 years ago • A.Barden

div class="preformatted">Dear bioconductor list, I am studing the Weaver experiment example of LIMMA manual and I am in a maze about the biological meaning of interaction term present among the contrasts. I did not manage

limma weaver limma weaver

updated 16.3 years ago • Erika Melissari

<div class="preformatted">Hi limma users!!! Does anyone know why and how a different weight value for flagged spot vastly influence significance levels(for both p-value and log odds) and order in topTable() list? I flagged spot with a self-made script for genePix(taking into acconunt some quality parameter like Signal to noise ratio and so on...) After I've used different values as weight…

limma limma

updated 19.9 years ago • daniela.marconi@libero.it

<div class="preformatted">Hi, I am having problems fitting a model (paired design with multiple factors) using limma, I have tried different ways of specifying the design and contrast matrix, but I stuck in the middle somewhere, so I post them here, maybe someone have already worked it out and know how to properly fit this: I have data from 10 animals, sampled at two different time points …

affy limma affy limma

updated 15.1 years ago • Huang, Tinghua [AN S]

I wish to analyze microarray data for identification of DEGs through limma analysis at the threshold P<0.05 or a fold change >1.5. I written R script as  results<-decideTests(fit2, p.value

limma microarray DEGs p values lfc

updated 8.5 years ago • rkp

The data distribution is poisson-like distribution. I have several question with regard to use of LIMMA package for the my purpose: 1) In general, Is the limma an optimal method to use for this kind of data and my purpose? 2) If this

limma

updated 2.8 years ago • Sep

Hi All, We have come across somewhat unexpected behavior from voom! / limma that is worth sharing. We found that using the same data, but different design matrices, "equivalent" contrasts...Hi All, We have come across somewhat unexpected behavior from voom! / limma that is worth sharing. We found that using the same data, but different design&nbs…

limma

updated 10.2 years ago • Stephen Hoang

<div class="preformatted">Hi, I have some questions regarding some cDNA array data I've been asked to look at. The design is slightly different to the standard designs, in that independent biological replicates (different plants within the same experiment) have been hybridised to different arrays. Therefore there are biological dye- swaps but not technical ones. Array 1 - WT plant 1/Treate…

limma limma

updated 21.6 years ago • Matthew Hannah

div class="preformatted">Dear All, As it described in Limma User's Guide chapter 8.7 there are more than one approach to create the design and contrst matrices. I would like to focus

limma limma

updated 19.4 years ago • Ron Ophir

<div class="preformatted">Dear all! When I use LIMMA to analyze microarray data, I use Array Weight parameter. I have some questions about it. The command is: #array weight arrayw...div class="preformatted">Dear all! When I use LIMMA to analyze microarray data, I use Array Weight parameter. I have some questions about it. The command is: #array weight

Microarray Normalization limma Microarray Normalization limma

updated 15.8 years ago • GAO Yu

treatment of interest. The platform is the 4x44k Agilent whole mouse oligoarray. I am trying to use Limma to determine significantly differentially expressed probes over the whole time series. First, is it even possible...design is new to me. If it is, then I could still use some help. I read the section of the Limma User's Guide (2 Jan 2008) on Dye Swaps, Technical Replication and Time Course …

Microarray Normalization limma Microarray Normalization limma

updated 17.4 years ago • Matt Huska

I have been using limma to perform linear regression to find genes differentially expressed with age, also include sex in the model. Here is

limma linear model

updated 7.5 years ago • KCLiv

<div class="preformatted"> Dear all, I am receiving an error when running the topTable function within the limma package, and I am having trouble deciphering its meaning. I would appreciate any feedback that could be provided! My data...preformatted"> Dear all, I am receiving an error when running the topTable function within the limma package, and I am having trouble deciphering its …

limma limma

updated 13.8 years ago • Monica Wong

17/02/2005 12:08:53 PM >>> 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

Annotation limma Annotation limma

updated 20.9 years ago • Marcus Davy

<div class="preformatted">Dear conductors, we are currently trying to see if we can reproduce the results of GeneSpring analysis using Bioconductor/limma and we are wondering what the best interface is, i.e., at what point in the analysis to input the Agilent data (image, raw, Gene...currently trying to see if we can reproduce the results of GeneSpring analysis using Bioconductor/limma and…

updated 16.5 years ago • Robinson, Peter

I am analyzing RNA-Seq data from a drug response dataset. There, we have a timecourse experiment with the following experimental design: 3 timepoints: 4h, 24h, 48h 3 drugs (A,B,C) + 1 untreated control 3 replicates per drug-timepoints I would like to get differentially expressed genes for each timepoint compared to the untreated control. I have followed the limma-voom tutorial, and I get clos…

limma

updated 3.1 years ago • rina

the issue is not all my patient samples are matched and in all groups. I've decided to use limma, currently I understand duplicateCorrelation() can be used to account for missing matched patient samples? I've generated...the code below following the limma manual and other similar questions I've found online: ```r # reads is an expression matrix with columns as samples and rows...just be…

RNASeqData DifferentialExpression limma

updated 2.4 years ago • gld-bioinf

div class="preformatted"> Hi, My custom image result files do not have background readings. But limma's read.maimages ask me for it. How do I get around this? I tried lying to it by giving it some random numeric column in the

Normalization Normalization

updated 20.7 years ago • Guoneng Zhong

My question is, how would I incorporate the duplicate correlation aspect when defining the design in limma? Thank you for your reply and help. Yolande [[alternative HTML version deleted]] </div

Yeast Yeast

updated 17.4 years ago • Yolande Tra

Hi all, I'm currently analysing a microarray dataset, on which I'm trying to detect the difference of gene expression between responders and non responders to a treatment. Even after reading the Limma user guide and searching on the forum I'm not really sure which design matrix I should use for the comparison. Here is a simplified model of my dataset : cy3 cy5 …

limma design matrix gene expression

updated 6.9 years ago • Guillaume Robert