Bioconductor Forum

Hello, I am running my GeoMx Data with Standr, and it includes the "limma" package. I am incorporating the codes from these two websites, https://davislaboratory.github.io/GeoMXAnalysisWorkflow...articles/GeoMXAnalysisWorkflow.html#differential-expression-analysis-with-limma-voom-pipeline https://ucdavis-bioinformatics-training.github.io/2018-June-RNA-Seq-Workshop/thursday/DE.html a…

GeoMx limma DifferentialExpression

updated 17 months ago • sophie00824

class="preformatted"> Hi! I am trying to use Single Channel Analysis of Two-Color Microarrays using limma. This topic is briefly discussed in limmaGui and I have some dificulties using intraspotCorrelation. Could somebody

limma limma

updated 21.6 years ago • Mayte Suarez-Farinas

<div class="preformatted">Hi, all: I'm trying to read in intensity data in limma package. But I get the following error: > files <- dir(pattern="*\\.gpr") > RG <- read.maimages(files, source="genepix") Error in...div class="preformatted">Hi, all: I'm trying to read in intensity data in limma package. But I get the following error: > files <- …

limma limma

updated 22.3 years ago • Hua Weng

to a number of requests, I have added a new argument to the function makeContrasts() in the the limma package. The new argument will accept a set of contrasts as a character vector, thus facilitating the use of makeContrasts...x <- c("A-B","C-(A+B)/2") makeContrasts(contrasts=x,levels=c("A","B","C")) The change is in limma 2.7.9 which will be available from CRAN in a couple of days. Gor…

limma limma

updated 19.4 years ago • Gordon Smyth

<div class="preformatted">Dear R users, I try to use Limma package to analyze methylation databases generated from Agilent CpG Islanfds, but i dont know if this is relevant because...div class="preformatted">Dear R users, I try to use Limma package to analyze methylation databases generated from Agilent CpG Islanfds, but i dont know if this is relevant

limma limma

updated 15.6 years ago • Mohamed Lajnef

div class="preformatted">Hi, I would like to use limma do 2X2 factorial analysis for 2 color microarrays. There in an example in the usersfuide for one color Affymetrix arrays

limma limma

updated 17.8 years ago • Khan, Sohail

there a way to extract the variance within and between groups after fitting the linear model in the limma package? Thanks. Sohail Khan Scientific Programmer COLD SPRING HARBOR LABORATORY Genome Research Center 500 Sunnyside

limma limma

updated 17.8 years ago • Khan, Sohail

how to include the technical replicates in a correct way in the model using eBayes analysis in the Limma package, please? I am not sure if the following script is correct: library(affy) Data.mes <- ReadAffy() phenoData(Data.mes...vl) library(affyPLM) Data.mes.rma <- rma(Data.mes) e.mes.rma <- exprs(Data.mes.rma) library(limma) Data.mes.rma <- rma(Data.mes) design &…

limma limma

updated 18.3 years ago • Lana Teixeira Fernandes

div class="preformatted">Dear Ian, This is fixed in limma 1.6.12 available from http://bioinf.wehi.edu.au/limma. You can now use RG <- read.maimages(files, source="smd") for SMD raw...now. > >SMD changed the headers in these files some time ago (around 9/03). It's >possible limma has not caught up. (We switched from using database field >names to more hum…

Cancer Breast limma Cancer Breast limma

updated 21.6 years ago • Gordon Smyth

<div class="preformatted"> >Date: Thu, 1 Dec 2005 18:44:24 +0100 >From: "Dr. D. P. Kreil" <dpkreil at="" gmail.com=""> >Subject: [BioC] limma: semi-bug (?) report for toptable >To: bioconductor at stat.math.ethz.ch > >Dear limma-maintainer, > >Firstly, thank you for providing limma, it has helped our work a lot. > >…

limma limma

updated 20.1 years ago • Gordon Smyth

<div class="preformatted"> Dear Bioconductor users, We are submitting our results to a journal and the reviewers ask us to reanalyze our data showing which p adjusted values have the genes that we selected. Our data have four different experimental groups (GEO number GDS1883), with three arrays for each group: -Healthy untreated animals: HU1, HU2, HU3 -Diabetic untreated animals: DU1, DU2, …

limma limma

updated 16.9 years ago • Jordi Altirriba Gutiérrez

Mar 2007 11:12:45 +0800 (CST) >From: zhaodj at ioz.ac.cn >Subject: [BioC] two questions about limma >To: bioconductor at stat.math.ethz.ch >Message-ID: <2959.159.226.67.50.1173150765.squirrel at mail.ioz.ac.cn...members, >I encounter two problems when analysing the microarray data employing the >package limma. I am using R ver.2.4.1 and limma ver.2…

Microarray limma Microarray limma

updated 18.8 years ago • Gordon Smyth

div class="preformatted">Hello everyone, I am trying to use Limma for microarray background subtraction and marray for normalization. To do this, I need to transfer my data between...for limma) and marray objects. I think that using limma for background subtraction and marray for normalization is standard, so...my previous data-processing scheme was reasonable, so there must be something I'm …

Microarray Normalization limma marray Microarray Normalization limma marray

updated 4.9 years ago • Ellen Sebastian

I am currently learning to do differential expression analysis on bulk and pseudobulk RNAseq data with limma::voom. In the [function documentation][1] it says > Note that [edgeR::voomLmFit][2] is now recommended over voom for sparse counts...am currently learning to do differential expression analysis on bulk and pseudobulk RNAseq data with limma::voom. In the [function documentation][1…

edgeR limma voom RNASeq muscat

updated 2.1 years ago • annikagable

div class="preformatted">Dear BioC, I am tring to use Limma package in order to analyze miRNA expression. I would like to identify differentially expressed miRNA; my experimental

miRNA limma miRNA limma

updated 18.6 years ago • claudio.is@libero.it

div class="preformatted">Dear all, I am trying to run vsn from Limma (R version 2.6.0 (2007-10-03)) Here is my code and the return: > essai2=normalizeBetweenArrays(essai,method="vsn") vsn: 2007

vsn limma vsn limma

updated 17.8 years ago • Catherine Juste

gt; statmod is deliberately a "suggests" rather than a "depends" because > only a small number of limma functions use it. > > As far I remember, there the Bioconductor install behaviour hasn't > changed. Maybe I misremember...However, you can use biocLite to install Suggests. Here are a couple ways to do this: biocLite("limma", dependencies=c("Depends", "Suggests…

Cancer limma Cancer limma

updated 18.7 years ago • Seth Falcon

div class="preformatted">Hi, I am using limma for background correction and normalization of two-color arrays. I have encountered a problem that I do not quite understand...46 47 Other subtraction methods (eg. "subtract") work well. I am running limma 2.4.4 on R 2.2.1 Any idea what is going wrong here? Best, Georg </div

Normalization limma Normalization limma

updated 19.9 years ago • Georg Otto

<div class="preformatted">Hi, I've been trying to use LIMMA to analyze a set of single channel data created with Agilent 105k arrays. I'm still learning R, so apologies if there is actually a very simple programmatic solution to my problem - but despite a lot of searching and reading I haven't been able to figure it out. By reading through various posts on this list (and of course the lim…

GO probe limma GO probe limma

updated 16.5 years ago • Marcel Dinger

From: weinong han <hanweinong at="" yahoo.com=""> >Subject: [BioC] What wrong with my data using LIMMA >To: bioconductor at stat.math.ethz.ch > >Hi. List, > >17 samples(3 normal samples, 14 NPC tumor samples from different...microarray experiments. The small size > >microarrays were recommmended to be analyzed using LIMMA. After &g…

Microarray affy limma affyPLM Microarray affy limma affyPLM

updated 20.3 years ago • Gordon Smyth

<div class="preformatted">To Whom it may Concern, I'm would like to inquire about the appropriate model design in limma for the model below. All patients are healthy, female and lean. Patient Tissue 1 Blood 1 Adipose Tissue 1 Buccal Cells 1 Lymph node 2 Blood 2 Adipose Tissue 2 Buccal Cells 2 Lymph Node 3 Blood 3 Adipose Tissue 3 Buccal Cells 3 Lymph Node We have…

limma limma

updated 12.9 years ago • Tim.Peters@csiro.au

div class="preformatted">Dear list, I'm using the limma package and the arrayWeights function to make some transcriptomic analysis: One group of samples versus an another...It seems that the weights are in general higher for the first group. Is that a problem? Next in limma, when Weights calculated by arrayWeights are implemented to the the lmFit function how are calculated the log2 fold

probe limma probe limma

updated 13.4 years ago • Amos Kirilovsky

div class="preformatted">Dear all, I would like to use Limma to read in not only the signal and background value, but also to read in additional spot data (spot quality flags, in this...the best way to do this? Secondly, is there a particular reason why the mean signal is read in into Limma, but the median background is read? I would like to be able to read in the median spot intensities. Aga…

limma limma

updated 21.9 years ago • Edo Plantinga

<div class="preformatted">When I created the design matrices in the original Weaver example, I just created the design matrices myself using cbind(). You could however use modelMatrix() using the 'param' argument to specify what you want the coefficients to represent. Gordon On Wed, June 1, 2005 1:32 am, Wenbin Liu said: > Thanks, Gordon! In the expanded example, you have a &g…

limma weaver limma weaver

updated 20.6 years ago • Gordon Smyth

Tue Sep 04 14:42:30 2012 I can get a more meaningful error if I install the development release of limma; useDevel() biocLite("limma") system.time(MA <- normalizeWithinArrays(RG, method="printtiploess", bc.method="none")) Error...0 1 8362 10070 The error appears to be caused in R core->stats:::simpleLoess (not limma) when interfacing C code, and I can see there have been …

Normalization limma Normalization limma

updated 13.3 years ago • Marcus Davy

<div class="preformatted">Hi all, I am trying to use Limma for multiple regression. The design matrix is like this : EffectA EffectB 1 25 0 35 0 28 1 32 The Effect A is categorical, The...div class="preformatted">Hi all, I am trying to use Limma for mult…

Regression limma Regression limma

updated 13.5 years ago • yao chen

div class="preformatted">We are analysing a cDNA microarray dataset in LIMMA with the following design and we run into "Coefficients not estimable" comments. R = 2.9.0 limma=2.18 We have two groups...If so, is there a way that we can keep the information on biological replicates and still use LIMMA? This is the contrast we were planning to use (which of course does not work) cont.matrix &am…

Microarray limma a4 Microarray limma a4

updated 16.1 years ago • Aubin-Horth Nadia

<div class="preformatted">You need to state the versions of R and limma that you are using. See "While sending mail to the list": Item 4 of the posting guide at http://www.bioconductor.org/docs/postingGuide.html...div class="preformatted">You need to state the versions of R and limma that you are using. See "While sending mail to the list": Item 4 of the posting guide at http://w…

limma arrayMagic limma arrayMagic

updated 20.2 years ago • Gordon Smyth

<div class="preformatted">Thanks Naomi, This is what I have been doing, but as I said, this is very laborious (especially when you have 50-200 arrays per project). I was hoping within limma there was an easy way of doing this, it seems like a very straightforward thing to implement, and a dedicated command for...this is very laborious (especially when you have 50-200 arrays per project). I …

limma limma

updated 21.6 years ago • Simon Melov

data by yourself and you want use the control probes for > the normalization, then you might try limma neqc function which can infer > the intensities of negative control probes using regular probe intensities > and...is there are two files available at NCBI GEO. This is the actual study GSE25001 but I want to use LIMMA package on their data. I see both raw data and normaliz…

Normalization probe limma Normalization probe limma

updated 14.7 years ago • Prasad Siddavatam

I have a performed a typical differential expression analysis using limma voom and I want to extract the log cpm values to draw ROC curves. But I want to extract the log cpm values produced specifically...by limma because they are normalised and free of batch effect that was added to the design matrix. Is there a function to do that

limma edgeR RNASeq

updated 20 months ago • Shaimaa Gamal

Dear list, I have RT-PCR data on 4 genes and 85 samples. Can I use 'limma' on this small set of genes? I want to use limma rather than usual paired t-test because I have missing values and I don

limma pcr

updated 7.5 years ago • Sandhya Pemmasani Kiran

div class="preformatted">I am unsure how to interpret the M-value produced by limma topTable when analyzing a multi-factoral, multi-level experiment. As an example, suppose I test one gene under the same

limma limma

updated 20.2 years ago • Kimpel, Mark W

div class="preformatted">Hi, I'm using R 1.9.0 and limma 1.5.6 (latest win32). I ran the following commands and got this error. >files <- dir(pattern="*.spot") >RG <- read.maimages

limma limma

updated 21.8 years ago • Matthew Hannah

same culture. The design was made this way for frugality. So in total we have 8 samples. I read the limma user guide and there was no example of such design. There are duplicate spots in each array but in random fashion so there

Microarray limma Microarray limma

updated 16.9 years ago • Yolande Tra

From: Sabine Trochim <sabine at="" biosolveit.de=""> >Subject: [BioC] Problem with write.fit in limma package >To: bioconductor at stat.math.ethz.ch > >Hi, > >I get an error message when trying to store a fitted model...in round(x, digits): non-numerical argument for mathematical >function" > >As I am using limma for the first t…

limma limma

updated 20.4 years ago • Gordon Smyth

gt; From: Naomi Altman <naomi@stat.psu.edu> > > Subject: [BioC] F-tests for factorial effects - limma > > To: bioconductor@stat.math.ethz.ch > > > > I am analyzing a 2-factor factorial Affy experiment, with 3 d.f. for...gt; > > I would like to get the F-tests for the main effects and interactions using > > l…

Microarray affy limma Microarray affy limma

updated 21.0 years ago • Naomi Altman

loaded into R as NChannelSet data. I cannot sort out how to get this into a format acceptable by limma. It's easy enough to access the channels as well as annotations but limma methods such as (for example) limma's normalizeWithinArrays...convert routines will convert to NChannelSet but not from NChannelSet to other types such as used by limma (RGList, MAList). I am tempted to now write the dat…

limma convert ArrayExpress SJava limma convert ArrayExpress SJava

updated 16.3 years ago • Chris Fjell

genes are down-regulated, than up-regulated is expected from our knowledge of the experiment. In the limma Users Guide (6 Oct 2005) p21, it says that loess does not assume equal number of genes up- and down-regulated, so this should...board(Aug 11 2004), but since I don't know much about the subject, I'm not very eager to change the limma code (I think that is what he suggest). How can I fix thi…

Genetics Normalization limma GeneSpring limmaGUI Genetics Normalization limma GeneSpring

updated 20.1 years ago • Cecilia McGregor

on the slides I'm currently trying variations of the command as outlined on page 9 of the Limma users guide M <- fit$coef A <- apply(MA$A, 1, mean) plot(A, M etc......) However taking into consideration the duplicates. The lengths

limma limma

updated 22.3 years ago • Jason Skelton

div class="preformatted">Dear all, I am analizyng Agilent G4121A mouse chips with LIMMA. My first three problems: 1) Layout: from the GAL file provided with the chip (and from the flat output file), I can only obtain

Normalization limma Normalization limma

updated 21.4 years ago • Giovanni Coppola

to analyze some old data obtained with the technology: miRCURY LNA from Exiqon. I use routinely limma and lumi package to anlayze Illumina BeadChip microarray but is the first attempt to analyze data obtained form this...2 are control and 2 are cancer patients (Hy3 and Hy5) What I would like to do now is to use limma package to assess for differential expression between the two groups but I a…

miRNA Microarray Cancer limma lumi ExiMiR miRNA Microarray Cancer limma lumi ExiMiR

updated 12.0 years ago • Paolo Kunderfranco

<div class="preformatted">Dear Developers This is my first time writing to your mailing list and I apologise if this should be handled in another way . I would like to report what I believe is a mistake in the documentation of the read.maimages package, part of the limma library. On the second paragraph of the "Details" on the help section the Agilent Background estimates description is…

limma limma

updated 13.2 years ago • Duarte Molha

<div class="preformatted">Hi everybody, I have a question regarding comparing limma and 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 devia…

Microarray limma Microarray limma

updated 11.6 years ago • Giovanni Bucci

so I have 6 expression vectors: A1, A2, B1, B2, B3). How do I write the design matrix to tell limma that A1 and A2 etc are technical replicates and that I want to do all pairwise comparisons between groups (ie. AvsB, AvsC...BvsC)? The limma manual covers technical replicates for two-channel arrays, and the multi-group experiments with biological replicates

limma limma

updated 15.8 years ago • Adam Kiezun

Nov 2005 17:09:09 -0600 > From: "Cecilia McGregor" <cmcgre1 at="" lsu.edu=""> > Subject: [BioC] limma Normalization question > To: bioconductor at stat.math.ethz.ch > > Hi Everyone > > I've described my experiment...are down-regulated, than up-regulated is expected from our knowledge of the experiment. > In the limma Users Guide (6 Oct…

Genetics Normalization limma GeneSpring limmaGUI Genetics Normalization limma GeneSpring

updated 20.1 years ago • Gordon Smyth

<div class="preformatted">Dear Dario, In truth, limma shouldn't need to know the layout for "control" normalization. I'll change the code to remove the check in the future. In the...<div class="preformatted">Dear Dario, In truth, limma shouldn't need to know the layout for "control" normalization. I'll change the code to remove the check in the future. In the meantime, you can s…

Annotation Normalization Cancer limma Annotation Normalization Cancer limma

updated 14.9 years ago • Gordon Smyth

trivial question. Inspired by the "export html report" in the limmaGUI. Is it possible to export a limma html report in the R shell ? morten</div

limma limmaGUI limma limmaGUI

updated 21.2 years ago • Morten

div class="preformatted">Hello, do I have to adjust for the group size when using LIMMA in case that one group has ~1000 samples and the other group has 3 samples? Best Regards, Daniel </div

limma limma

updated 13.9 years ago • Enx Enx

to have given this information. Please reply to the mailing list. Best wishes Gordon >[BioC] limma question >Sun, Yezhou yezhou.sun at mssm.edu >Wed Feb 22 23:27:27 CET 2006 >Hi, there, > >I am using limma for some single

Microarray limma convert Microarray limma convert

updated 19.9 years ago • Gordon Smyth

I am a very new user of R and hope you can help. I have tried the fora and online help. I am using limma to analyse microarray data. I have run into a problem with GeneSetTest which i don't understand, but think it is something...only numeric characters ( and when run with a dummy "sel" set is fine) when I run this: library(limma) > sel<-sub.2 > stat<-sub.3 > ge…

Microarray limma Microarray limma

updated 14.1 years ago • Esther Robinson

<div class="preformatted">Dear Saroj, This isn't a solution to your general question about ..., but makeContrasts in limma already accepts character vector arguments: x <- c("a-b","b-c") makeContrasts(contrasts=x, levels=c("a","b","c")) Best wishes Gordon &gt...Dear Saroj, This isn't a solution to your general question about ..., but makeContrasts in limma already acce…

limma limma

updated 16.6 years ago • Gordon Smyth

div class="preformatted">Hi, I am new to limma and am having problems reading Scanarray Express .csv files into limma via read.maimages. I am running R version 2.4.1...and limma version 2.9.17. I tried... >RG<-read.maimages(files, source="scanarrayexpress", path=path) Error in readGenericHeader

limma limma

updated 18.7 years ago • sltucker@artsci.wustl.edu

<div class="preformatted">Dear all, Following the RMA normalization of data from Affy Human Exon ST1.0 array using the package Oligo (at the transcript level using target="core"), I then conducted a limma analysis. The topTable argument in limma would then retrieve the top genes (in my case, cause I am interested in subsequently doing GSEA analysis, I set number=100) which are differentia…

Normalization affy limma biomaRt oligo Normalization affy limma biomaRt oligo

updated 12.6 years ago • Jeremy Ng

div class="preformatted">Hi, we are trying to analyze 52 chips, with 4 treatments in Limma. They load up fine, boxplot, etc. Design is ok, but when we run > fit <- lmFit(MA, design) Error: (subscript) logical subscript...not sure what this means, and would appreciate any help. Our other arrays and analysis works fine in limma, but we havent input this many arrays into limma bef…

limma limma

updated 21.9 years ago • Simon Melov

class="preformatted">Hi! I would in a microarray experiment analyze three factors simultaneously in Limma, treatment, group (i.e. gender), and study center. Is it possible to include three factors simultaneously in an interaction

Microarray limma Microarray limma

updated 12.6 years ago • Ingrid Dahlman

<div class="preformatted"> > Date: Thu, 06 Oct 2005 12:40:32 +0300 > From: "Ron Ophir" <ron.ophir at="" weizmann.ac.il=""> > Subject: [BioC] [limma] Factorial refernce design > To: "<bioconcutor" <bioconductor="" at="" stat.math.ethz.ch=""> > > Hi, > I work with dual channel technology and I would like to use limma for >…

limma limma

updated 20.3 years ago • Gordon Smyth

<div class="preformatted">> Date: Sun, 2 Jan 2005 14:05:15 -0800 (PST) > From: "Fangxin Hong" <fhong@salk.edu> > Subject: [BioC] A question about Limma > To: bioconductor@stat.math.ethz.ch > Message-ID: <1867.66.75.240.64.1104703515.squirrel@66.75.240.64&gt...05:15 -0800 (PST) > From: "Fangxin Hong" <fhong@salk.edu> > S…

PROcess Microarray limma

updated 2.6 years ago • Gordon Smyth

Hello community, I was running Limma on RNA array expression data and am confused about the output of Limma toptable(). One of the columns is called LogFC, but...I want to report Log2FC. After searching some Bioconductor posts and the Limma vignette, I've found conflicting reports on where Limma is reporting a true LogFC or Log2FC. Can someone help clarify...If Limma output is a true LogFC, u…

limma R ExpressionData

updated 3.0 years ago • Keith

pearson squared, and same p-value as above, also produces coefficients lm(exprs(esetgcrma)[1,]~num) #limma - produces the same coefficients as lm() above design <- model.matrix(~num) fit <- lmFit(esetgcrma,design) So limma produces...in R is also capable of regression fits. > Looking (but not > >understanding) lm.fit in limma, it appears to be an independent &…

GO Regression limma GO Regression limma

updated 21.4 years ago • Matthew Hannah