Bioconductor Forum

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

Dear Bioconductor Community, as I'm currently writting a report about my gene expression analysis on two affymetrix microarray datasets, regarding differential expression, i found an paper (http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0012336) mentioning the necessary assumptions and "possible requirements" in order to use different categories of statistical tests. In my case…

limma statistical inference variance test bioconductor

updated 10.6 years ago • svlachavas

<div class="preformatted">Hello, I would like to use limma to carry out single channel analyses on some two color data (to address comparisons that can't be made with standard methods and my unconnected experimental design). I'm able to get two color analyses to work nicely but run into problems when I try to run the single channel analysis using the 'lmscFit' function (as described in the…

limma limma

updated 20.8 years ago • Brett Abrahams

Hi, everyone. I have performed my in Limma package because there are nested effect interaction (random effect) in statistical model. Looking to my results the

limma RNAseq foldchange

updated 6.8 years ago • susana.amaral.teixeira

reference. Numbers indicate the technical groups. I already wrote a piece of R code based on the limma users guide but I am not sure if I did it well (I am not an statistician) Could you please tell me if the script below is correct...if not, how may I change it? Thanks in advance, ...and thanks to Dr. Gordon Smyth and cols. for limma package! The R code: ------------------------------------…

limma limma

updated 18.2 years ago • Juan C Oliveros Collazos

Dear list, I use Limma to determine differential expression between classes. My question concerns how to find class specific coefficients...for one or all probes. Three questions: 1) can i extract CV values "automatically" when using the Limma package to find differential expression? 2) if not, at what stage would I be able to use the standard deviations and mean

limma coefficient of variation cv

updated 10.3 years ago • nils.rudqvist

Hello, The topic of this email looks easy enough, but I cannot find in the Limma documentation how the (log2) fold changes are actually calculated. As you probably now, Limma uses log2-scaled input (originating...method, unlog, calculate the mean, and log2-transform again, is the proper way and I do expect that Limma does it the same way. My question is: is this true? Regards, Dr. Philip de…

limma

updated 8.8 years ago • Groot, Philip de

I am analyzing a very large RNA-Seq experiment (100s of samples). I intend to use limma for the analysis, mainly due to the speed of limma compared to edgeR or DESeq2. I specifically want to keep a large number...stable, with only a few samples outside the recommended 3-fold range, so I also looked at using the limma-trend approach. I was unable to find any info on the how limma-trend behaves wh…

limma voom limma-trend

updated 9.2 years ago • maltethodberg

Goscik and I work as an assistant at the Bialystok Technical University, Poland. I am quite new to limma package and a little bit confused about reading data into the R environment. The data I am trying to analyze has the following...files - six different arrays - two channel data The commands I use to read data is: > library("limma") > setwd("P:\\dane"); > targets=readTa…

limma limma

updated 16.2 years ago • Joanna Goscik

<div class="preformatted">I apologize in advance, since I only started using limma 2 days ago. I have a simple experiment with 2 treatments (S and F) in a loop design. For each treatment I have 3 biological replicates...div class="preformatted">I apologize in advance, since I only started using limma 2 days ago. I have a simple experiment with 2 treatments (S and F) in a loop design. For…

Genetics limma limmaGUI Genetics limma limmaGUI

updated 20.2 years ago • Cecilia McGregor

div class="preformatted">Following up on a thread I initiated last year on missing values in limma and contrasts.fit (see gmane.science.biology.informatics.conductor:26494 gmane.science.biology.informatics.conductor...at reed.edu ====================================================================== === library(limma) ### necessary files and data are at: url <- "http:/…

limma limma

updated 15.4 years ago • Albyn Jones

class="preformatted"> Dear all, Hello, I'm a student, and I want to analyse my microarray data with limma GUI but the program bug probably because my data isn't in a good format. My data comes from the software Array-Pro Analyser...the dye-swap. I haven't background data (the correction was done by Array-Pro). For input my data in limma GUI, I create this 2 text files : > > Spo…

Microarray GUI limma Microarray GUI limma

updated 21.4 years ago • hélène régé

for separate channel analysis. I just want to add that following the brief procedure outline in Limma User Guide wasn't useful. I have made the targets file as usual FileName Cy3 Cy5 1 US83800208_252412610022_1_4.txt...is the right one for this kind of analysis and second If there is a kind of filter I can use in limma to get rid of those neg intensities to proceed to the next step. Thanks …

Normalization limma PROcess convert Normalization limma PROcess convert

updated 13.9 years ago • jgomez@uni-potsdam.de

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2058, this is a two sample array data, can limma used for this? thanks a lot

limma

updated 5.3 years ago • linouhao

<div class="preformatted"> Dear bioconductors, Forgive me if this is in the limma user's guide, but I'd like to be able to find the top, say, 100 probe sets in topTable sorted by M, not abs(M). I understand that I...div class="preformatted"> Dear bioconductors, Forgive me if this is in the limma user's guide, but I'd like to be able to find the top, say, 100 probe sets in topTable sort…

probe limma probe limma

updated 20.8 years ago • Cyrus Harmon

<div class="preformatted">Dear Nataliya, > Date: Fri, 11 Nov 2005 01:09:48 +0100 > From: Nataliya Yeremenko <eremenko at="" science.uva.nl=""> > Subject: [BioC] Design question in LIMMA > To: Bioconductor List <bioconductor at="" stat.math.ethz.ch=""> > > Hello > This is a long letter about my efforts of analysis of data in Limma…

Normalization limma a4 Normalization limma a4

updated 20.2 years ago • Gordon Smyth

Feb 2007 14:22:41 +0100 >From: Ben Nota <be.nota at="" ecology.falw.vu.nl=""> >Subject: [BioC] limma lmFit error >To: bioconductor at stat.math.ethz.ch >Message-ID: <45D30D20.7030309 at ecology.falw.vu.nl&gt...1; format=flowed > >Dear BioC, > >I'm getting an error using the lmFit function within limma. I'm using R >2.…

limma limma

updated 18.9 years ago • Gordon Smyth

<div class="preformatted">Dear Lorenzo, limma uses all the arrays in your experiment to estimate the residual standard errors, not just the arrays that you specify in your contrast. In your second analysis, it appears that you are analysing only a subset of the arrays. If you do this, all the results will change, because the number of residual degrees of freedom uses to estimate the stand…

Microarray limma Microarray limma

updated 15.2 years ago • Gordon Smyth

Hello, I have a question about filtering lowly expressed probes (or genes) when using limma. For the example in section 17.4 of the limma user's guide, probes are called expressed if they exceed a cut-off in more than...p/52762/) warning against filtering based on variance because it would affect the limma algorithms, but I am not sure whether this is quite the same thing. Would this be …

limma filtering

updated 8.7 years ago • jamie.gearing

<div class="preformatted">Aha! Thanks for the tip - am getting gene names now! And thanks for the look-see at my script. Cheers, Lisa -A couple of corrections. Background correct is yet doing everything it -should with EList objects, so the background subtraction has to be done -manually. And I now see why you're not getting gene names in your -toptable. You can use - - x <- …

Annotation Bayesian limma PROcess Annotation Bayesian limma PROcess

updated 15.4 years ago • Orfe, Lisa

BioC, Please guide me in experient..Howmany Cells I need to collect in order to be confident in my LIMMA statistical analysis? I think LIMMA is the good approach because I hvae more than 2 conditions. Please see below information

limma limma

updated 20.6 years ago • SAURIN

div class="preformatted">Dear all, I am currently working with gene expression analysis in limma. I have a total of 146 samples divided into 21 groups. What I want to do is pairwise comparisons between one group (the control...to 203 before for the GroupB-GroupControl comparison after the BH correction. Is there a possible limma specific explanation for this? I have read the documentation on…

limma limma

updated 11.5 years ago • Arvid Sondén

div class="preformatted">Hi, In limma, one can use decideTests to assign each gene up/down/NC coded as 1/-1/0, and then use vennCounts to count the number of genes

limma ASSIGN limma ASSIGN

updated 19.9 years ago • He, Yiwen NIH/CIT

<div class="preformatted">Hello, I am very new to R programming. I am trying to read the data from Genome Studio output using Limma package. I am able to do so by: >x <- read.ilmn(files="path.for.probe", other.columns="Detection") >x$other gives me the detection...Hello, I am very new to R programming. I am trying to read the data from Genome Studio output using Lim…

limma limma

updated 14.7 years ago • Rahul Maurya

I am using limma-voom to determine the change in the change of gene expression between men and women due to a treatment. I have previously...global", "nestedF", or "hierarchical"? (https://bioconductor.org/packages/release/bioc/manuals/limma/man/limma.pdf pg.50) Any help would be greatly appreciated! Thank you

limma limma voom limma contrast matrix multiple testing correction

updated 8.8 years ago • gregory.l.stone

I am analyzing the TCGA data and doing the differential expression analysis for about 6,000 samples and 20,000 coding genes. I was suggested to use DESeq2 for DE analysis, but the DESeq() takes an extremely long time with 6,000 samples, therefore I would like to use the limma-voom instead. In the tximport [vignette](https://bioconductor.org/packages/devel/bioc/vignettes/tximpor…

tximport limma deseq2 differential expression

updated 7.4 years ago • mico

div class="preformatted"> I am trying to colour a limma generated MA plot by fold change. I can do it this way: status <- bugs.colour(RG,1) attr(status,"values") <- c("nonsignificant

limma limma

updated 15.8 years ago • adam_pgsql

twofold up or down compared to control) that are common in at least 9 of 10 sample group I used LIMMA in R.  My code <pre> samples <- as.factor(samples) design <- model.matrix(~0 + samples) fit <- lmFit(exprSet, design) contrast.matrix...results, "results1.txt", sep="\t", quote=FALSE)</pre> I compared the  logFC  generated by …

limma LogFC

updated 9.7 years ago • beginner

in CpG methylation between the two groups? Attempting to answer my own question, it looks like limma can help me. But I don't see any clear workflows/pipelines online that explain how to incorporate and control for co-variates...in design matricies created for limma. Can someone point me to a pipeline that can offer me guidance for what I want to do? if not, any general suggestions or tip…

minfiDataEPIC arrays limma minfi Epigenetics

updated 5.1 years ago • jefflincoln4

all, please if I may ask a question that may have been asked before, it is  about basics of limma and edgeR : sometimes in the documentation and in some examples, the design matrix is specified as : 1) design <- model.matrix

limma edgeR

updated 8.9 years ago • Bogdan

Dear all, We are using limma to perform differential expression analysis among 3 different groups. The problem (or not) is that the design is unbalanced

limma statistical power design variability microarray

updated 8.2 years ago • roser.navarro

using affy /simpleaffy. Could you please send me the code or hints to fit this normalized data to LIMMA in R-package. I would be glad and highly appreciate for your kindness. source("http://www.bioconductor.org/biocLite.R...biocLite("limma") biocLite("affy") library(affy) setwd("/home/haojamrocky/DATA/GSE11024") rawdata<-ReadAffy() eset <- expresso(rawdata, normalize.method

affy limma GLAD affy limma GLAD

updated 14.0 years ago • 하오잠 로

16 columns and 11 rows each mir has 4 replicates For analysis of the data I use limma GUI, to obtain the p-values of differentially expressed mirs I carried out loess normalization (backgroundsubstraction...column-distance, using the number of spots of row distance results in dims[product 0]). I read the limma guide and checked also the examples on the limma gui homepage, but …

GUI limma microRNA GUI limma microRNA

updated 17.3 years ago • Christine Voellenkle

Mon, 20 Feb 2006 12:58:15 +0100 > From: Ana Conesa <aconesa at="" ivia.es=""> > Subject: [BioC] Limma: bad spots flagged out? > To: bioconductor at stat.math.ethz.ch > Message-ID: <7.0.0.16.0.20060220124132.02020ff0...I have a doubt about the real use of spots weights during > normalization in limma. According with the documentation s…

Normalization limma Normalization limma

updated 19.9 years ago • Gordon Smyth

div class="preformatted"> Hi limma users. I have some general questions regarding the use of dupcor.series and gls.series functions. I use an experimental...matrix, and if so, how would it look like. During these analysis I have used R-version 1.8 and limma version 1.3.1 I would be very grateful for some response. Regards Marcus **********************************************************…

Pathways limma Pathways limma

updated 22.2 years ago • Marcus

div class="preformatted"> >[BioC] limma 2.2.0 - decideTests heirarch/nestedF + BH correction , small bug >Ariel Chernomoretz ariel.chernomoretz at crchul.ulaval.ca...n > 70 ) On the other hand, this is a bug. It has been fixed already in limma 2.3.6, but thanks for reporting it anyway. Unfortunately the bug is still in Bioconductor release 1.7, but…

limma limma

updated 20.1 years ago • Gordon Smyth

scans to line 60! Is there a way to get around this using other methods? I would prefer to do it in Limma because I wish to be able to show my colleague how to do analysis with this package. Kind Regards Ben Routley [[alternative

limma limma

updated 20.8 years ago • ben

div class="preformatted">Dear all, When I use the limma function decideTests() with method="nestedF" to dertermine the differentially expressed genes, I encounter an error

limma limma

updated 18.2 years ago • De-Jian ZHAO

2 by 2 these groups using for instance LPE >or another test like this one, > option (2) using Limma. LPT is the "local pooled error test" proposed in a papery by Jain et al, http://hesweb1.med.virginia.edu/bioinformatics...research/index.html, which is apparently to appear in Bioinformatics. Limma and LPT address the same problem but from different points of view. Scanning the pa…

Normalization affy limma LPE PROcess Normalization affy limma LPE PROcess

updated 22.3 years ago • Gordon Smyth

08 +0200 > From: Christelle Dantec <christelle.dantec at="" igf.cnrs.fr=""> > Subject: [BioC] limma: duplicateCorrelation > To: bioconductor at stat.math.ethz.ch > Content-Type: text/plain > > Hi, > > I have a technical...gt; Christelle Dear Christelle, It would appear from the error messsage that you are not using limma directly but…

Normalization Normalization

updated 19.6 years ago • Gordon Smyth

I am VERY new to R/Bioconductor and over the past two weeks have managed, I hope, to put together a limma script to process my single color generic arrays. I was hoping that some of the experts that read these posts could comment...you would process a home-made single color array? If not, I would LOVE some pointers. >library(limma) >targets <- readTargets("targets.txt") &a…

Bayesian limma PROcess Bayesian limma PROcess

updated 15.4 years ago • Orfe, Lisa

Hi, I noticed that both edgeR and limma have function to perform differential splicing analysis based on exon level counts. I am wondering why exon level...Hi, I noticed that both edgeR and limma have function to perform differential splicing analysis based on exon level counts. I am wondering why exon level counts...used instead of splice junction counts (i.e. STAR SJ output). Would it be …

splicing limma edgeR

updated 21 months ago • scoops_streams_06

<div class="preformatted"> Hi, I'm approaching a RNA-seq experiment concerning the analysis of a time course of 5 time points in 6 experimental groups (including Control group). As an example: FileName Group Time a Control 6hr b Control 24h . e ExpG1 6hr f ExpG1 24hr l ExpG2 6hr m ExpG2 24hr ... (ExpG1, ExpG2 are experimental groups) I'm going to use LIMMA for extraction of time changin…

limma limma

updated 12.0 years ago • Riba Michela

Hi all, I'm using limma to analyze a proteomics dataset, basically following the approach described [here][1], so log2(count+1), quantile normalization...then a limma pipeline with eBayes(trend=TRUE, robust=TRUE). However, I was wondering if it is possible to use `vooma` on the data somehow

limma proteomics voom

updated 4.3 years ago • Endre Sebestyén

human biopsies (2 groups, 50 samples each). My pipeline is trimmomatic-star-featureCounts-edgeR-voom/limma (big fan of limma, being a veteran from array days..). <span style="line-height:1.6">I am looking into the optimal ways to filter...my data to increase detection power. Thus far, I have used the method from the limma manual to filter by cpm in >50 samples. I have stumbled over …

limma edger sequencing

updated 9.4 years ago • blofeld

Dear Limma/EdgeR users, I have 2 treatment groups, 3x biological replicates for each. I also have 2 extra samples, a pool of each treatment...23/bioinf-seminar-gordon-smyth.html In addition, a recent publication also promotes the use of voom-limma over other methods due to False Positive Rates.  http://biorxiv.org/content/early/2015/06/11/020784 <span style="line...mind, I want to…

limma voom edger

updated 9.3 years ago • Johnny H

ve earlier used > > rowttests and FDR > > > correction. Now I was playing around with limma to see what > > I could do > > > (added different covariates etc) but also investigated the > > most simple > > &gt...setting, comparing the two different stages directly using > > Limma. The…

hgu133plus2 affy limma gcrma hgu133plus2 affy limma gcrma

updated 17.5 years ago • Boel Brynedal

gt; Date: Wed, 29 Jun 2005 09:54:11 +0200 > From: kerick at molgen.mpg.de > Subject: [BioC] limma: decideTests, which option to chose? > To: bioconductor at stat.math.ethz.ch > > Dear all, > > to the best of my knowledge...deep enough. > I am seeking advice on which option to choose from the decideTests function in > limma. Since the …

limma limma

updated 20.5 years ago • Gordon Smyth

div class="preformatted">Hi all, I have used limma before for differential analysis but only for very simple experiments comparing two conditions. I am helping a colleague...wildtype vs mutant using the levels "female" "male" "mu"? I have read through the examples in the limma user guide but the answer is not obvious. Thanks for any help. Ed [[alternative HTML version deleted]] <…

mouse4302 limma mouse4302 limma

updated 12.1 years ago • Ed Mountjoy

<div class="preformatted"> Hi again, sorry to be a bother but one more question. After knowing that lets say 20 genes are being used for the PCA would it be possible to figure out how much each gene contributes? So to develop an equation or know specifically in PC1 the variance in these x genes were the most important or something? .kripa > From: dwu@fas.harvard.edu > To: tt…

limma limma

updated 13.6 years ago • Kripa R

the processed data and model results, but I'm confused about the model interpretation. [Page 44 of limma's user guide describes the exact model used in this study][2], a paired sample with a block size of two. The code for this is...take a look it can be found [here][5]. Thank you for your time! # Code from page 45 of the limma user guide SibShip <- factor(targets$SibShip) …

limma microarray

updated 5.8 years ago • jdougherty

This can be done using the limma33 package in Bioconductor. Therefore, I did regularization on Limma, but I'm not sure if this is correct. So, I want to ask everyone to confirm my command below. #use data in nature protocal #create...subset(bg_chrX,"rowVars(texpr(bg_chrX)) >1",genomesubset=TRUE) #make design for limma design <- model.matrix(~0+sex+po…

limma ballgown RNA-seq

updated 6.0 years ago • komuracom16

2006 16:09:16 -0800 >From: "Karen Vranizan" <vranizan at="" berkeley.edu=""> >Subject: [BioC] limma duplicateCorrelation question >To: <bioconductor at="" stat.math.ethz.ch=""> >Content-Type: text/plain > >The following

limma limma

updated 19.1 years ago • Gordon Smyth

mail, I have four arrays in a replicated dye swap experiment. After carrying out the analysis in limma, I find that 360 out of 4600 genes have an unadjusted p-value <= 0.05. However, when I adjust these using adjust="fdr", all of

limma limma

updated 21.0 years ago • michael watson IAH-C

Dear list, I have a simple doubt concerning how I should deal with the *replicate day* effect using limma. It is clear that I have a *day effect* in my data that it has to be taken into account in the model. I am using 2 different model

limma limma

updated 19.5 years ago • Pedro López Romero

div class="preformatted">Dear Bioconductor users, I just began to use limma package for the analysis of microarray data. I want to include in the analysis two factors (treatment and time) and the

Microarray limma Microarray limma

updated 11.9 years ago • David Moriña Soler

<div class="preformatted">Hi, I have been given a bunch of data; some of it is from a 384x164 chip and another that is 532x85. First question, how can I read these in and normalize them together? I can create separate target files for each set. But then how to merge? I have seen the limma section title 'Combine RGList, MAList, EList or EListRaw Objects', but since there are different rows …

limma limma

updated 14.4 years ago • Brent Pedersen

<div class="preformatted">Yi: Could you send the output of sessionInfo() to the list? I am attaching mine at the end. I guess that you are using an old version of limma (when field dimensions had only one block). It is recommended to upgrade to a more recent version (e.g., 2.10.5). > so read.imagene() calculates the total number of spots as prod(FD): > nspots <- prod…

limma limma

updated 18.5 years ago • Saroj Mohapatra