Bioconductor Forum

I have a question on limma differential testing on proteins. <https://bioinformatics.stackexchange.com/questions/4850/why-do-i-have-this-perfect...volcano-plot-from-limma> I have the script that can reproduce the plot in the link. My question is why Limma would generate the volcano plot as described

limma

updated 7.4 years ago • SmallChess

I am using limma on GSVA scores to assess differential expression of gene sets (in microarray and RNAseq data). Since GSVA scores can...I am using limma on GSVA scores to assess differential expression of gene sets (in microarray and RNAseq data). Since GSVA scores can be...negative, I am wondering how limma calculates the fold changes between a negative and a positive GSVA score and how meaningf…

limma gsva

updated 6.8 years ago • rocanja

<div class="preformatted">Dear limma users, I have an experiment designed as follows: Samples were taken from 3 individuals(S1, S2 and S3), and for the sample from...div class="preformatted">Dear limma users, I have an experiment designed as follows: Samples were taken from 3 individuals(S1, S2 and S3), and for the sample

limma limma

updated 20.4 years ago • Wenbin Liu

them all together using lumi; vst followed by quantile normalisation. I have then gone on to use limma to get the topTables for each of the comparisons that I make. The script works well and produces everything that I wanted

limma limma

updated 15.6 years ago • Taylor, Katie

div class="preformatted">Hi all, I have been using limma now for a couple of weeks, and I think I have pretty much got the hang of most of it. However, now I want to analyse a slightly

limma limma

updated 22.2 years ago • Pete

genome" human arrays (~18,000 genes) for a couple years and I have helped with the analysis using Limma. Now, due to costs, they are now considering switching from whole genome arrays to focused arrays with ~400 genes of interest...would be willing to include 100-150 genes that are not expected to change. 2. The B-statistic in Limma requires a parameter indicating a certain fraction of genes ar…

Normalization limma Normalization limma

updated 20.6 years ago • Mike Schaffer

<div class="preformatted">Hello, Can anyone tell me if there is an R function available for producing Venn diagrams? I came across a description of the limma package that indicated that it contained a Venn diagram function - but it appears to be missing from the 1.3 release. Thanks...if there is an R function available for producing Venn diagrams? I came across a description of the limm…

limma limma

updated 22.1 years ago • John Fieberg

div class="preformatted">Hi, I am trying to use limma to analyze Mass Spec data for differentially expressed proteins from wild type cell and mutant cells. The input data

limma limma

updated 19.6 years ago • yuhong ning

experiment is very similar to Swirl experiment given in tutorials). I tried normalising data with "limma" package with following commands: library(limma) Warning message: package limma was built under R version 1.8.1 RG&lt

Microarray graph limma Microarray graph limma

updated 21.8 years ago • Binita Dutta

<div class="preformatted"> > Date: Mon, 08 May 2006 17:17:50 -0400 > From: CHUNFA C JIE <cjie1 at="" jhmi.edu=""> > Subject: [BioC] question on decideTests function in limma > To: bioconductor at stat.math.ethz.ch > Message-ID: <27808c9c2329e.445f7d3e at jhmimail.jhmi.edu> > Content-Type: text/plain; charset=us-ascii > &am…

Microarray limma Microarray limma

updated 19.6 years ago • Gordon Smyth

<div class="preformatted">Hello everyone, I'm trying to compare limma vs edgeR in finding tissue specific genes from my RNAseq samples. For edgeR I've followed directions from a previous post and have managed to get good results. The thread is named "edgeR: finding tissue specific genes" and here is the link: http://permalink.gmane.org/gmane.science.biology.informatics.conductor /47950 Ho…

RNASeq limma edgeR RNASeq limma edgeR

updated 12.5 years ago • Jaaved Mohammed

<div class="preformatted">Dear bioconducter mailing list I am a PhD student in plant breeding department in Norway. I am using your limma package for analyzing my RNA-seq data. Since I am not a statistician, so I am asking you a very small question from you. I have a 2 factorial experiment with a split plot design, where block was the main plot and lane was in sub plot. Now I want to fit t…

RNASeq Microarray limma RNASeq Microarray limma

updated 12.2 years ago • sci yasmin

div class="preformatted">Hi, I need help with analysis using the limma package. Here is the experiment design: 20 patients, 10 on a regular diet and the other 10 on a special treatment diet. For...both before/after treatment and day1/day6. I am at lost as how to create a design matrix and call limma for such a study design. Can someone please help? Thank you very much. Yiwen He BIMAS/CIT/N…

limma limma

updated 13.2 years ago • He, Yiwen NIH/CIT

div class="preformatted"> Hi, In limma there is this plot function: plotMA3by2 It's great. But it doesn't seem to allow me to assign a file name. And it ignores any

limma ASSIGN limma ASSIGN

updated 7.0 years ago • Guoneng Zhong

div class="preformatted">I am trying to use limma to import a series of bluefuse post processed files. This is the command I am using: CGHraw <- read.maimages(CGHFiles...only contain the genes that pass the QA and so different files have different probes. I believe that limma finds all the common probes between the files and then only imports for them. I would like to do the reverse,…

Cancer probe limma Cancer probe limma

updated 17.8 years ago • Daniel Brewer

<div class="preformatted">Dear Tobias, When you claim that software has a bug, you need to give a code example which others can run, so that we can see what you mean. Here's an example of such code. This example which shows that all the different normexp variants in backgroundCorrect() give similar but slightly different results, just as they are supposed to. Note that mle gives the bes…

limma limma

updated 16.2 years ago • Gordon Smyth

div class="preformatted">Sorry I'd been away and missed some posts - it seems limma - fdr is a hot topic at the moment. To link this to an answer already provided by gordon - this is the thread I found earlier...contrasts then genes vs. the reverse? I'd also be interested in the discussion of how quantitive limma p-values are (see point 4 in previous mail below). On these lines - from the a…

limma limma

updated 21.4 years ago • Matthew Hannah

<div class="preformatted">Hi everybody, I have a question regarding comparing limma to the t-test. I compared the p values obtained from both algorithms using 100 samples in each condition. Given the large number of observations my expectation was to see high correlation between the p values. As shown below, I ran the same code in three different conditions for the mean and standard deviat…

Microarray limma Microarray limma

updated 11.6 years ago • Guest User

Hello,   I've performed gene set enrichment analysis with the limma-package's camera -function. I'm using limma's barcodeplot -function to visualize my results (one index set, no gene weights...Hello,   I've performed gene set enrichment analysis with the limma-package's camera -function. I'm using limma's barcodeplot -function to visualize my results (one index set, no gene…

limma gene set enrichment analysis

updated 7.2 years ago • khandarius

gt; >Rather an odd title, but here goes... > >Basically I have read in my data in both limma (using read.maimages) and >marrayInput (using read.marrayRaw). > >I want to normalize my data using loess normalisation...First point: I did a lot of work about a month and half ago to speed up the loess normalization in limma considerably. As a result, limma no l…

Normalization limma PROcess Normalization limma PROcess

updated 22.4 years ago • Gordon Smyth

div class="preformatted">Dear Gordon Smyth, bioconductor list, In the limma package we found a function called, removeBatchEffect, which removes the effects of batch effects or other technical...sva package as an alternative, but as this function also only accepts categorical variables, this limma function seems like a better option to modify its code for our purpose. Regards, Djie Thung B…

limma limma

updated 9.5 years ago • Djie Tjwan Thung

for any advice. I have a difficulty in constructing the contrast matrix of factorial design in limma. In section 8.7 of limma user's guide, a factorial design is discussed. My experimental design resembles the example very

limma limma

updated 17.7 years ago • De-Jian ZHAO

for any advice. I have a difficulty in constructing the contrast matrix of factorial design in limma. In section 8.7 of limma user's guide, a factorial design is discussed. My experimental design resembles the example very

limma limma

updated 17.7 years ago • De-Jian ZHAO

<div class="preformatted">Hello list I'm being a bit stupid with romer (for GSEA) in the limma suite. In order to run the analysis I need to indicate in each gene set I have which row in my expression data that gene belongs...div class="preformatted">Hello list I'm being a bit stupid with romer (for GSEA) in the limma suite. In order to run the analysis I need to indicate in each gene …

limma limma

updated 15.2 years ago • Iain Gallagher

div class="preformatted">Hi, Is it possible to correct for batch effects in limma when doing a paired analysis? I have pairs from two runs Batch 1 and Batch 2. There  are no pairs where one is in Batch1

limma limma

updated 13.7 years ago • khadeeja ismail

div class="preformatted">Hi, I'm new to R, and i want to use the R software package Limma to compute some tests for differential gene expression. However, my data is in a matrix-style format (with the Huber variance

limma limma

updated 17.5 years ago • Markus Seto

Hi, I want to use limma removeBatchEffect(covariate = tumor_purity) to correct my protein intensity values (log2 transformed) for the continuous...variable of tumor purity. I am wondering if limma is built to do this properly and I am asking because when I corrected a particular gene (log2 transformed before correction

limma

updated 8 months ago • gabriella.jacobson-eisenberg

<div class="preformatted">Dear Lisa, limma now has a representation for single colour arrays (ELists), so you can simplify your pre-processing code somewhat: E <- read.maimages(targets,columns=list(G="Median",Gb="MedBackground "),green.only=TRUE) E$genes <- read.delim("Annotation file.txt",stringsAsFactors=FALSE) E <- backgroundCorrect(E, method="subtract") E …

Bayesian limma PROcess Bayesian limma PROcess

updated 15.4 years ago • Gordon Smyth

<div class="preformatted">Dear Pedro, The strategy you are proposing is to ignore experimental factors which you think will have relatively small effects, so as to generate some degrees of freedom for error. This is an ok strategy, long used in statistics, as long as you understand clearly what you are testing for. If you do this, limma will try to find genes which have differential expres…

genefilter limma genefilter limma

updated 19.8 years ago • Gordon Smyth

Hi all I was wondering what a good cutoff is for a truely expressed probe in the limma data analysis (single channel agilent): \#filter out expressed probes from background signal: control type probes neg95...lt;- matrix(1.1\*neg95,nrow(G.norm.quant),ncol(G.norm.quant),byrow=TRUE) This was based on the limma user guide: I took 110% of the 0.95 percentile of the control probes expression per…

limma background signal

updated 11.2 years ago • wim.trypsteen

datasets from array express. I have been reading lots of posts relating to obtaining DE genes from limma. A lot of people seem to carry out DE in limma and then select DE by using __both__ logFC (absolute > 2 /1.5) and FDR pvalue...However i have read that this might not be suitable and that by using the treat function in limma this takes into account the fold change when computin…

limma treat

updated 8.9 years ago • danielle.newby

trained and untrained side of the CNS. Each pair is hybridized to one two-color array. With the limma user guide and Google, I came up with the following script which seems to give quite reasonable results: library(limma...GeneSpring. In GeneSpring I ended up with ~400 transcripts regulated at with a FDR of 0.05. With limma, though, I get nearly 1,000 at FDR = 0.01! Many of these, though, h…

qPCR limma GeneSpring qPCR limma GeneSpring

updated 11.9 years ago • Calin-Jageman, Robert

Hi, Does anyone know how to get the loading scores for MDS plot in limma? So, for example in the following example code in the plotMDS in limma, I'd like to know the contribution of each of the simulated...Hi, Does anyone know how to get the loading scores for MDS plot in limma? So, for example in the following example code in the plotMDS in limma, I'd like to know the contributio…

plotMDS limma

updated 2.5 years ago • Cen

that situation, there is no way to assess statistical significance relative to biological variation. limma has ways of making use of technical replicates, but there needs to be biological replication as well. Best wishes Gordon...of using any > statistical method to analyse their data. Am I right or is it possible > to use limma in such a case? > > Kind regards, &…

limma limma

updated 15.8 years ago • Gordon Smyth

to rational target selection from my data mining work. So far most of my analysis was done with ```limma```, and I came across a published study where the group shared their result generated from ```DESeq2```. and the questions are...1) How translatable are the DEG results calculated from ```limma``` and ```DESeq2```? 2) is it appropriate if I pool the DEGs identified with ```DESeq2``` or ```l…

DESeq2 limma

updated 23 months ago • Lily Cheang

div class="preformatted">Is there a mistake on p. 67 of the Limma User's Guide (27 October 2004)? Firstly, MA.pq is not defined, but the density is plotted. Secondly, we have normalizeWithinArrays

limma limma

updated 20.5 years ago • Naomi Altman

<div class="preformatted">Dera Abdul, We use GenomeStudio in order to export probe summary profiles and control summary profiles which are then read into the limma package. GenomeStudio doesn't do any downstream statistical analysis, as far as I know, comparable to limma. To see what limma does, see the User's Guide: http://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst …

probe limma probe limma

updated 12.7 years ago • Gordon Smyth

recommend the preprocessing pipeline for Illumina data given in Case Study 11.7 on page 91 of the limma User's Guide. The beadarray code you give does not appear to be doing any background correction. You could call "neqc" as...function in beadarray, but that does not give the same results as calling neqc() directly in limma. Best wishes Gordon > Date: Sun, 17 Apr 2011 13:12:48 +0200 &a…

Annotation Preprocessing limma beadarray Annotation Preprocessing limma beadarray

updated 14.7 years ago • Gordon Smyth

data set using the "normalizeWithinarrays" and the the "normalizeBetweenarrays" function within Limma. I know the Convert package could convert limma and marray data objects. is there any ways to convert a table format object

limma marray convert limma marray convert

updated 21.1 years ago • Caimiao Wei

preformatted">I have noticed that I get exactly the same number of sig. t-tests when using the limma function classifyTestsP when using both methods="none" and methods="fdr". Delving a little deeper, I performed the function

limma limma

updated 21.4 years ago • Kimpel, Mark W

div class="preformatted">In the limma manual, 27 October 2003, near the bottom of page 3, the output from the command topTable(fit, n=30, adjust="fdr") shows a column

limma limma

updated 22.2 years ago • Dick Beyer

old microarray data we have (dye-swaps!). I can go through the workflow fine as recommended in the limma guide, however, I'd really like to generate some lineplots of the expression. We have quite a lot of arrays per group, and

Microarray GO graph limma Microarray GO graph limma

updated 13.2 years ago • Simon Melov

preformatted">Dear BioC List Members: I have a data set that I would like to analyze with the limma package. I am having trouble figuring out how to make the design and contrasts matrices, and I was hoping that someone...even after normalization. Specific questions that I am hoping to have answered: 1. Can I use limma to remove the batch effect that I have observed with the third replicate? …

Normalization limma Normalization limma

updated 21.2 years ago • Jim Breaux

<div class="preformatted">Hi, I work with dual channel technology and I would like to use limma for two way analysis. My experiment is as follow: FileName Cy3 Cy5 GL_251322310100_S02_.gpr WT3h NI3h GL_251322310101_S02_.gpr WT3h NI3h GL_251322310103_S02_.gpr Mut3h NI3h GL_251322310104_S02_.gpr Mut3h NI3h GL_2513…

limma limma

updated 20.3 years ago • Ron Ophir

gt; To: BioConductor List <bioconductor at="" stat.math.ethz.ch=""> > Subject: [BioC] Colouring limma MA plot > > > I am trying to colour a limma generated MA plot by fold change. I can do > it this way: > > status <- bugs.colour

limma limma

updated 15.8 years ago • Gordon Smyth

amp; gcrma return log2 values, while li-wong and mas5 results are unlogged. I'm pretty sure that limma wants logged data, but how about multtest? Thanks in advance, Ken</div

limma gcrma limma gcrma

updated 21.0 years ago • Ken Termiso

<div class="preformatted">Hi, I have a question concerning the analysis of some affymetrix chips. I downloaded some of the data from GEO GSE11324 (see below). In doing so I'm stuck after I identified the probesets with significant changes. I have problems in assigning probeset specific gene names as well as getting the genomic coordinates. Furthermore I have no clue how to deal with the fa…

Clustering affy limma Clustering affy limma

updated 15.8 years ago • Maxim

Hello dear community, There has been a similar post: "modeling heteroscedasticity in limma-voom for RNA-Seq data analysis" but the topic was different. I have proteomics data over time, so every row of my matrix...Hello dear community, There has been a similar post: "modeling heteroscedasticity in limma-voom for RNA-Seq data analysis" but the topic was different. I have proteomics dat…

limma splines Proteomics

updated 8 months ago • Thomas

<div class="preformatted">Dear TS, You are wanting to select genes which satisfy several conditions. There is no way to do this with a single contrast. You need to compute all three contrasts and then select genes: cm = makeContrasts(ON=ON-WT, KO1=KO1-WT, KO2=KO2-WT, levels=design) fit <- lmFit(data, design) fit2 <- contrasts.fit(fit, cm) fit2 <- eBayes(fit2) results …

limma limma

updated 19.1 years ago • Gordon Smyth

I am analyzing RNA-seq data, and I have tried both the voom and robustified limma-trend approaches (following the process outlined in [RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR][1] and...reviewing the user's guide), but the p-values do not agree very well. After adjustment, the robust limma-trend approach results in more significant transcripts than voom, and there is only mo…

limma limma-trend voom RNASeq

updated 4.1 years ago • Tyler Sagendorf

Hi, Just comparing the output of limma and lme. The model that I fit with lme is : <pre> le <- lme(lmIntensity ~ Condition, random = ~1|Donor, data = x) </pre> Since I have...Hi, Just comparing the output of limma and lme. The model that I fit with lme is : <pre> le <- lme(lmIntensity ~ Condition, random = ~1|Donor, data = x) </p…

limma linear model paired samples

updated 8.6 years ago • wewolski

div class="preformatted"> Hello All I am having some difficulty in trying to use limma for a paired analysis. Can anybody suggest an approach that would work? The arrays are Affymetrix. The experiment arrays...but with the Placebo or Drug treatments reversed. How can this be analysed? Looking at the Limma User Guide 8.3 Paired Samples looks to be a good start. But is it possible to do so…

limma limma

updated 17.3 years ago • john seers IFR

<div class="preformatted">> Date: Mon, 31 Jan 2005 09:56:09 -0500 > From: Naomi Altman <naomi@stat.psu.edu> > Subject: [BioC] limma - FDR adjusted "p-values" > To: bioconductor@stat.math.ethz.ch > > Just a suggestion: > > The FDR adjusted "p-values" are...Mon, 31 Jan 2005 09:56:09 -0500 > From: Naomi Altman <naomi@stat.…

GO limma GO limma

updated 20.9 years ago • Gordon Smyth

<div class="preformatted">> I have a question regarding what weighting function to use when > analyzing Agilent data with limma. My > question is whether or not it makes sense to down-weight the control > probes? > > > As far as I can see, the normalization methods don't make explicit > use of the control probes and hence I would &…

Normalization limma Normalization limma

updated 14.0 years ago • Maciej Jończyk

hello sir, i have gpr files. can someone tell me how to write script for limma containing gpr files

limma

updated 8.2 years ago • krithi11987

if things can be done better. (Its a 3 sets of dye-swaps with 2 spots per orf per chip) library(limma) targets<-readTargets("targets.txt") RG<-read.maimages(targets$FileName,source="genepix",wt.fun=wtflags(0)) RG$printer...background from foreground and flagging negative numbers. This is obviously the default for limma. BUt when doing this approach, a lot of spots popped up that…

limma Category limma Category

updated 20.7 years ago • lepalmer@notes.cc.sunysb.edu

model selection, then limma is probably not the tool > for the job. > > Instead, what I would do would be to choose some (one, five, ten, > whatever) genes...selection steps, and once you are > satisfied with the model you have chosen you can go back to limma and > fit the model on all the genes. > > Best, > > Jim > &…

GO limma PROcess GO limma PROcess

updated 16.1 years ago • Yannick Wurm

Hello, I am using limma to determine differential gene expression between healthy and KO mice. I know that there is a very strong batch effect...on this forum and on _Biostar_ that it is generally recommended to include the batch effect in the limma model instead of using for example _Combat_seq_ to adjust for the batch effect. I wanted to make sure that limma can appropriately...effect inc…

BatchEffect limma sva DifferentialExpression

updated 3.9 years ago • nhaus

<div class="preformatted">Dear list members, short version of my question: How can I determine, whether it improves the model quality of a linear model (in limma), when I introduce additional explanatory variables? Is there an equivalent to feature selection (as in machine learning) for choosing the explanatory variables? The complete story: We analyse a dataset of about ninety single cha…

Microarray limma Microarray limma

updated 16.4 years ago • Andre J. Aberer

<div class="preformatted">Dear list, can anybody suggest how could I insert gene names in additional to gene symbols on my topTable generated by limma with my differentially expressed genes? cheers, Marcos B. Pinho Programa de Engenharia Química - PEQ Laboratório de Engenharia...suggest how could I insert gene names in additional to gene symbols on my topTable generated by limma with my d…

limma limma

updated 16.3 years ago • Marcos Pinho