Bioconductor Forum

<div class="preformatted">At 03:12 AM 6/08/2004, Richard Friedman wrote: >Fellow Expressionists, > > Does Limma automatically perform a multiple >comparison adjustment for non-orthogonal contrasts? Yes. classifyTestsF() is a...At 03:12 AM 6/08/2004, Richard Friedman wrote: >Fellow Expressionists, > > Does Limma automaticall…

Bayesian Classification limma bridge Bayesian Classification limma bridge

updated 21.4 years ago • Gordon Smyth

From: qq bioconductor <qq.bioconductor at="" gmail.com=""> > Subject: [BioC] Error when running limma on low variance data > To: bioconductor at stat.math.ethz.ch > Content-Type: text/plain > > Dear list member, > &gt...I got an error message when running limma on my array dataset, which > contains a total of four Affy arrays from two dif…

affy limma affy limma

updated 16.3 years ago • Gordon Smyth

<div class="preformatted">I am new to using limma. I have a set of 2-channel experiments that I have an interest in comparing. All are with respect to a common reference. The...div class="preformatted">I am new to using limma. I have a set of 2-channel experiments that I have an interest in comparing. All are with respect to a common reference

limma limma

updated 22.2 years ago • Sean Davis

Hi I have performed print-tip loess normalisation followed by quantile normalisation in limma. I have then converted the resulting MAList object back to an RGList object using RG.MA(). I now want to extract the single

limma limma

updated 21.3 years ago • michael watson IAH-C

Sent: 14 November 2004 02:36 To: bioconductor@stat.math.ethz.ch Subject: [BioC] Confusion over limma documentation and design/contrast matrix >Date: Fri, 12 Nov 2004 13:42:22 -0000 >From: "michael watson (IAH-C)" <michael.watson...bbsrc.ac.uk> >Subject: [BioC] Confusion over limma documentation and design/contrast >To: "Gordon Smyth" <smyth@wehi.edu.au> &a…

GO Regression limma GO Regression limma

updated 21.1 years ago • michael watson IAH-C

<div class="preformatted">Hi Naomi and list, some time ago I asked a question on how to model an experiment in limma. I think I need some additional help with it as the experiment grew in complexity. I also added a factor "batch" because the arrays were run in separate batches, and I think would be good to control for it. The dataframe with phenotypic informations ("dummy") looks like this…

affy limma affy limma

updated 16.7 years ago • Paolo Innocenti

2005 09:31:00 -0600 >From: "Hua Weng" <hweng at="" biochem.okstate.edu=""> >Subject: Re: [BioC] Limma toptable question >To: <bioconductor at="" stat.math.ethz.ch=""> > >Dear Bioconductor: > >There are two reasons that...smyth at wehi.EDU.AU] >Sent: Tuesday, November 29, 2005 3:12 PM >To: Hua Weng >Subject: Re:Limma…

Microarray Regression limma Microarray Regression limma

updated 20.1 years ago • Gordon Smyth

I have a dataset with 10 condition vs 20 control samples and am using limma to test for differential expression. Broadly, groups are age/sex matched but have added noise due to complex medical...which are matched as best as possible but is still far from perfect. Ran through a basic analysis limma pipeline, everything worked as expected. In the same batch, I processed a number of other sample…

limma multtest

updated 12 months ago • Ali Barry

to get comparison of interest? What I tried and what I will do are like the following, library(limma) targets2 <- readTargets("Targets2.txt") RG<-read.maimages(targets2$FileName, source="spot",wt.fun=wtarea(100)) RG$genes...statmod Attaching package 'statmod': The following object(s) are masked from package:limma : matvec vecmat Error in chol(ZVZ + lambda * I) …

GO limma ASSIGN GO limma ASSIGN

updated 21.2 years ago • Ren Na

Hello, I'm trying to use the LIMMA package in R Studio, and am having trouble using the plotDensities command.  I am able to plot the densities of all...commands such as plotDensities(MA, arrays=c(1:5)).  A colleague using earlier versions of R and LIMMA was able to produce plots of individual arrays using these commands, but with the most recent version of R Studio, only

limma microarray

updated 11.1 years ago • alison

at r-project.org]? > <bioconductor at="" r-project.org=""> > Subject: [BioC] How is LIMMA actually calculating the average > expression value? > > Dear all: > I have found quite the same question being asked...at least twice but I > still not have clear answer about how the ebayes method in LIMMA > calculate the average ex…

probe limma gcrma probe limma gcrma

updated 12.6 years ago • Gordon Smyth

<div class="preformatted">Dear Sunny, > Date: Mon, 27 Sep 2010 03:14:01 -0400 > From: Sunny Srivastava <research.baba at="" gmail.com=""> > To: bioconductor <bioconductor at="" stat.math.ethz.ch=""> > Subject: [BioC] Question: How does limma derives its logFC value in > two colored arrays? > > Hello Bioconductor Gurus, …

Yeast affy vsn limma Yeast affy vsn limma

updated 15.3 years ago • Gordon Smyth

have limma_1.8.16, not sure if someone needed to know that CRAN is not up to date with respect to limma. I downloaded 1.8.21 from Gordon's site. Peter</div

limma limma

updated 20.9 years ago • Pita

Dear BioC community, is it possible with LIMMA to test for equivalence of expression between two sample groups? I am thinking about two one sided test (TOST) or double

limma differential gene expression equivalence TOST DOSTT

updated 10.9 years ago • Andreas Heider

in and do normalization of cDNA microarray data with format as .txt or .xls by marray package or limma. Thanks in advance! Darwin --------------------------------- Yahoo! Search - Find what youre looking for faster. [[alternative HTML version deleted]]</div

Microarray Normalization limma marray Microarray Normalization limma marray

updated 21.8 years ago • rwin qian

<div class="preformatted">I know this topic has arisen a few times from searching the mail archive, but I'm still not clear on what/how to do this. Here is my experimental setup: Array Param1 Param2 Rep Batch 1 H 4 1 1 2 H 4 2 2 3 H 4 3 2 4 H 20 1 1 5 H 20 2 2…

limma GeneSpring limma GeneSpring

updated 18.4 years ago • Nathan Haigh

knowledge of linear models is too restricted. The problem is that I want to do a paired t-test using limma, but that I want to fit multiple comparisons (using different patients!) simultanuously. The reason for this is that all...Treatment_Diet_2 103 My design matrix (for a paired t-test) is calculated as follows (from the Limma user guide): Replicates <- factor(pData(x.norm)$rep…

limma limma

updated 18.1 years ago • Groot, Philip de

div class="preformatted"> Hello Bioc members, I got a question about using limma to extract up-regulated genes from Affymetrix microarray datasets. I have created a design matrix, called lmfit, make

Microarray limma Microarray limma

updated 15.3 years ago • Victoria Hu

<div class="preformatted">Dear all, On running the eBayes function in LIMMA, I got the following error. > fit_NODS7 <- eBayes(fit_NODS7) Warning message: Estimation of var.prior failed - set to default...div class="preformatted">Dear all, On running the eBayes function in LIMMA, I got the following error. > fit_NODS7 <- eBayes(fit_NODS7) Warning message: E…

limma limma

updated 20.6 years ago • Ankit Pal

I'd like to use limma-voom to do a differential expression analysis on RNA-seq data using "my own" (i.e., external for limma) observation weights

limma limma-voom

updated 7.8 years ago • Peter Langfelder

Hi The limma t test function is very fast compared with using the R function with a for loop for large data sets. I want to use this t...Hi The limma t test function is very fast compared with using the R function with a for loop for large data sets. I want to use this t test

limma microarray

updated 9.8 years ago • chris86

<div class="preformatted">Dear All, I used limma with two different parametrizations. Both approaches should be equivalent in my opinion. However, if I use weights, the...div class="preformatted">Dear All, I used limma with two different parametrizations. Both approaches should be equivalent in my opinion. However, if I use weights...below. Does someone know the reason for this? Regar…

limma limma

updated 17.2 years ago • Hans-Ulrich Klein

<div class="preformatted"> > Date: Mon, 17 Jan 2005 15:12:12 +0100 > From: "Ingunn Berget" <ingunn.berget@umb.no> > Subject: [BioC] Limma, decideTests > To: <bioconductor@stat.math.ethz.ch> > > Hello mail-list > > Experiment > This microarray experiment was conducted to study gene expression in > bact…

Microarray limma Microarray limma

updated 20.9 years ago • Gordon Smyth

div class="preformatted">Greetings, I have been doing some RNA analysis with the limma package using the eBayes function. I have a matrix of counts consisting of 25322 genes and 23 samples. I intended to use

limma limma

updated 12.6 years ago • Charles Determan Jr

It is quite possible. Could it be that you are comparing multiple- testing adjusted p-values from limma with unadjusted p-values from another program? >4) As i understand from your explanation i have to >top<-topTable

Normalization limma Normalization limma

updated 21.8 years ago • Gordon Smyth

Now fixed in R 2.16.3. Best wishes Gordon -------- original message ---------- [BioC] Problem with limma topTable Chen, Zhuoxun Zhuoxun_Chen at URMC.Rochester.edu Sat Nov 8 01:01:33 CET 2008 Dear Bioconductors, I came across

limma limma

updated 17.2 years ago • Gordon Smyth

BST) > From: Lev Soinov <lev_embl1 at="" yahoo.co.uk=""> > Subject: Re: [BioC] paired design, LIMMA > To: BioC Mailing List <bioconductor at="" stat.math.ethz.ch=""> > Message-ID: <802561.11912.qm at web27902.mail.ukl.yahoo.com...Lev. > > Gordon Smyth <smyth at="" wehi.edu.au=""> wrote: > >>[BioC] paired desig…

cdf tkWidgets affy widgetTools limma affyio cdf tkWidgets affy widgetTools limma affyio

updated 18.7 years ago • Gordon Smyth

div class="preformatted">Dear list, I am a new user to the limma package for differential expression analysis and have recently noticed that when I generated my toptable with the

limma limma

updated 16.3 years ago • Marcos Pinho

14 controls, 12 patients (fixed factor: group) i am mainly interested in the group effect! i tried limma, but it did not seem to work with my random factor patient?. any suggestions? thanks for help! tina -- Bettina Kulle Andreassen

ExpressionData limma ExpressionData limma

updated 17.5 years ago • Bettina Kulle Andreassen

are many ways to do this, I am wondering whether people has compared methods such as SAM, EBAM, and LIMMA by applying them to the same dataset. Of course, they have different assumptions and different models, but should they

limma limma

updated 20.8 years ago • Wu, Xiwei

A empty CellB_empty B empty</pre> An empty vector is used as control.  I ran limma-voom and DESeq2 to detect the differentially expressed genes. The following is a summary of the analysis: ## __Design__...the contrasts Vector1-Empty, .... Vector10-Empty. When pulled together, I obtained 36 targets with limma and 172 targets with DESeq2. Among them 8 are shared between…

normalization limma deseq2 counts

updated 10.0 years ago • Radek

div class="preformatted"> Hi Bioconductor users, has anyone published data using "limma" for microarray analysis and would point me to it? Thanks a lot, Julia</div

Microarray Microarray

updated 21.7 years ago • Julia Engelmann

<div class="preformatted">> Date: Fri, 29 Oct 2004 11:43:22 -0400 > From: Andr? Chanderbali <achander@botany.ufl.edu> > Subject: [BioC] reading Aglilent 60mer oligo data files into limma > To: bioconductor@stat.math.ethz.ch > Message-ID: <43B19B22-29C1-11D9-806C-0003938C4B2C@botany.ufl.edu> > Content-Type: text/plain; charset…

Genetics limma oligo Genetics limma oligo

updated 21.2 years ago • Gordon Smyth

Hi, I am trying to analyze human RNA-seq data with limma. I have two conditions: affected by disease and not affected. More concretely, I have mother (VAN012, not affected), father...have 2 replicates for each sample. My goal is to find DE genes in these two conditions. I am using limma for this task and after building MDS plot I see this pic: <img alt="" src="https://i.imgur.com/HMcGWNQ.png…

limma heterogenous human

updated 7.7 years ago • chipolino

to you for your attention to my questions. Special thanks to Dr. Smyth, the author and maintainer of limma package, for his detailed answer. However,questions remain. The two questions first appeared in Bioconductor Digest...RG$G <- RG$G + offset } new("RGList", unclass(RG)) } <environment: namespace:limma=""> The method normexp is within the function backgroundCorrect. It i…

Microarray limma Microarray limma

updated 18.8 years ago • De-Jian ZHAO

Dear Philip, You are seeing problems where really there are none. The advice from the limma User's Guide guided you correctly. Your limma session below is perfectly correct. Jim's advice was perfectly correct...t-test as a reference method which you believe you have to reproduce. The aim of linear modelling in limma is to give you the best possible test, not to reproduce the test statistic you …

Microarray GO Cancer limma Microarray GO Cancer limma

updated 18.1 years ago • Gordon Smyth

I'd like to make Venn diagram from Limma `decideTests` results. Limma `vennDiagram` function is limited to maximum of 5 sets. I tried to make the plot using `veneluer

limma venn diagram vennplot

updated 8.2 years ago • Seymoo

div class="preformatted">Dear BC list, I am using limma the first time. I have an unbalanced sample with 130 controls and 60 cases, should I correct for the different sizes? My

limma limma

updated 14.7 years ago • Babara Mueller

First, I apologize if these are dumb questions... I am new to R and Microarray data. That being said, I would appreciate any helpful feedback and/or links. From what I've read here, it is unusual to remove flagged data-points in limma and I couldn't find any post showing how to do it within the limma package (read.maimages does have a weight function, but it's not for Agilent data). That being s…

limma agilent

updated 7.8 years ago • CantExitVIM

for blank spots and the like, so the block has missing rows, and this causes a problem because the limma functions assume complete blocks. BTW, this is why the function read.maimages() didn't set the $printer information automatically...NAs in the right places, so that you could use imageplot(), but this bit of code is not provided by limma or Bioconductor. Try this: r <- stuff$genes$…

limma limma

updated 19.0 years ago • Gordon Smyth

would it be correct to interpret the results as follows: >p<-scan(pvalues.txt) > library(limma) > propTrueNull(p,method='lfdr'); \[1\] 0.02203173 All the pvalues in my vector p that are <0.022 are sig (pass the false positive

limma

updated 8.4 years ago • mrutyunjaya-parida

is not true if your MA object contains weights or missing values. For the design matrix you give, limma does indeed give unchanged coefficients in the absence of weights, missing values, blocking, and so on. Best wishes Gordon...jean-laurent.ichante at="" cgm.cnrs-="" gif.fr=""> > Subject: [BioC] Dye effect problem with Limma package > To: bioconductor at stat.math.ethz.ch &…

limma limma

updated 16.8 years ago • Gordon Smyth

<div class="preformatted"> Just for others that might have the same problem: the files were in the correct format (.txt) but I had to change them over from a MS-DOS Formatted Text (.txt) to Windows Formatted Text (.txt) or a Tab Delimited Text (.txt) to import them into R successfully. From: czammit@hotmail.com To: jmacdon@med.umich.edu Date: Wed, 8 Dec 2010 14:03:51 +0800 CC: bioconductor…

Microarray Annotation limma Microarray Annotation limma

updated 15.0 years ago • Carla Zammit

preformatted">Sorry, this is due to my lack of knowledge of R I suspect! I have an MAList object in limma containing several arrays. I access the column of M values thus: MAn[,3]$M Where Man is my MAList object. What I want to do is

limma limma

updated 21.4 years ago • michael watson IAH-C

I am trying to perform some linear regressions with respect to some covariates in limma so that I can predict expression values after controling for 2 covariates, `Afactor` and `Efactor`. Basically, this is my...a1` and `a2`, and `Efactor` is a factor with 3 unique values `e1`, `e2`, `e3`. To fit it, I'm using limma as follows: ```r design=model.matrix('~0 + Afactor + Efactor', my_metadata) fi…

limma

updated 4.2 years ago • rf

replicates (dye swap). Hence, my experiment is similar to your example in section 11.1 of the limma user's guide. Our array has four within-array replicate spots for each gene. As the "block" argument in the limma function

Microarray limma Microarray limma

updated 20.3 years ago • Pie Muller

div class="preformatted"> Dear Users, I am using Limma package to identify the DEGs, toptable() was used to define the adjusted p-value, now as project requested, it has to be selected

limma limma

updated 12.4 years ago • Guest User

<div class="preformatted">Hello, I'm analyzing human exon arrays normalized using Affymetrix Power tools for normalization (using 'core' probes) and limma for significantly modulated genes (all at the gene level, of course). The limma2annaffy function produce tables, but with...exon arrays normalized using Affymetrix Power tools for normalization (using 'core' probes) and limma for signif…

Normalization limma biomaRt oneChannelGUI Normalization limma biomaRt oneChannelGUI

updated 16.0 years ago • Michael Imbeault

Hello, I am testing what condition Limma can not be used and do some simulation (as below). I find that no matter one-color or two-color microarray, if only have __one...replicate__, Limma can be used to get the result. But if __no any replicate__, then Limma refuses analysis in the step : fit2 <- eBayes(fit2...nbsp; My question is: If in all arrays, just __one replicate__, ma…

limma microarray

updated 9.0 years ago • kevin.m.hao

div class="preformatted"> >[BioC] A limma question. >Johan Lindberg johlin at kth.se >Fri Apr 21 16:56:06 CEST 2006 > >I think this is kind of a stupid question

limma limma

updated 19.7 years ago • Gordon Smyth

Hi BioC community, I study the gene expression profiles of three groups by microarray data. The aim is to perform the pairwise comparisons of the three groups. The sample size of each of the group is n=10. GCRMA normalization and filtering were applied before using limma to perform differential analysis. Unfortunately, no gene is significantly differentially expressed after limma analysis (FDR…

limma sample size microarrays statistical power

updated 7.8 years ago • eleonoregravier

div class="preformatted">Hi All, I did a test run of Limma looking at the user's guide, on using the normalizeWithinArrays() function, I got a subscript out of bounds error. The steps

limma limma

updated 20.7 years ago • Ankit Pal

linear model? Is it because - the statistical theory is not ready? - or - it is not implemented in Limma? I am not a statistician so it might be a stupid question :-) Thanks Jakob ------------------------------------------------------------------- Jakob Hedegaard Danish Institute of Agricultural...BioC] random block effect and technical replicates within array at the same in linear model using…

Genetics limma Genetics limma

updated 20.6 years ago • Jakob Hedegaard

I'm a bit confused about the heatmap output from limma voom. For example, the image below shows RNAseq result of comparing ZnD samples to ZnR (control) samples. In the same limma

limma

updated 14 months ago • lhwh1208

I have seen many researchers use (and instruct on how to use) Limma for analyzing genomics data. What are the changes that need to be made to the way Limma is used for analyzing Proteomics

Limma Proteomics

updated 9.6 years ago • cookm346

gene is replicated 4 times on each array. I know how to fit blocks as random as explained in the Limma manual (Technical replication I) I know how to account for the replication within arrays. Is it possible to fit random...block effect and technical replicates within array at the same in linear model using Limma ? Thanks Peter</div

limma limma

updated 20.6 years ago • Peter Sørensen (HAG)

Hi, <span style="line-height:1.6">I have done a differential expression analysis using limma. When I try the camera analysis </span> <pre> <span style="line-height:1.6">dummy_out=camera(voom_data,all_signatures_for_camera

limma camera

updated 10.2 years ago • ea1402

I am trying to perform a differential gene expression of a big microarray data using Limma. I found roast is the function of choice for when the sample size is large. however, i have some problem for selecting or

limma microarray differential gene expression

updated 10.9 years ago • Nemo

Hello! I'm following the instructions shown in the limma user guide (17.4; page 113). The main objective of our project is to recover a list of DEG (from > 4 independents studies...Hello! I'm following the instructions shown in the limma user guide (17.4; page 113). The main objective of our project is to recover a list of DEG (from > 4 independents studies) and

ArrayExpress limma arrays

updated 4.6 years ago • RMP87

sizes (n < 4 per group), it is often better to perform regularization. This can be done using the limma package in Bioconductor._   How this can be done? First, do "regularization" and "normalization" has the same meaning

limma rna-seq

updated 8.1 years ago • zoukai3412085