Bioconductor Forum

fpkm, if so, how should I prefilter fpkm value, is there a recommendation and I hear someone said limma will give more false positive compared to edger and deseq2, is that true? here is the detailed code of trend and voom If...3-fold. In the limma-trend approach, the counts are converted to logCPM values using edgeR's cpm function: > logCPM <- cpm(dge, log=TRUE, prio…

limma

updated 5.3 years ago • linouhao

div class="preformatted">Dear All, I am now starting to do my microarray data analysis with limma. When I try to run the cases in chapter 11 of limma user?s guide, I can download Weaver mutant and Bob mutant data from http

Microarray limma weaver Microarray limma weaver

updated 17.6 years ago • Wang, Jixin

div class="preformatted"> Dear List: Recently, I used limma package to analyze some miRNA array data. One of the differential lists I derived for one of the contrasts in our limma...etc) (I used adj="fdr" in topTable...) although the other contrasts in the same model we set up in limma does have "normal" looking adj.P.Val ranged from 1 to about 0.01. >From our previous experience, so…

miRNA limma miRNA limma

updated 14.6 years ago • Yi, Ming NIH/NCI [C]

<div class="preformatted">Dear Jay, Thanks for pointing out this error. Mea culpa -- I recently noticed that lmFit() wasn't setting Amean for the marrayNorm objects, and in fixing this have in fact broken lmFit() for marrayNorm objects. I've fixed this for limma 2.9.14. In the meantime, you can use library(convert) lm <- lmFit(as(snorm,"MAList"), design=c(1,-1,-1,1)) Be…

limma marray limma marray

updated 18.8 years ago • Gordon Smyth

has released an R script that analyses microarray data and controls for the FDR. I notice also that limma controls for the FDR, and wondered if/how the two analysis methods compared, both in theory/philosophy and in practice

Microarray limma Microarray limma

updated 21.4 years ago • michael watson IAH-C

div class="preformatted">Dear List I've a very basic question about the limma output (and I'm newbie of MA analysis). I'm looking some analysis output .Usually in the M column (if I well understand ) I should

limma limma

updated 15.7 years ago • Guido Leoni

div class="preformatted">Dear limma developer and list: I am wondering if it is possible to extract something like anova table with group Pr. information

limma limma

updated 19.9 years ago • Jianping Jin

Gene2 Probe4 Gene2 Probe5 Gene2 Probe6 Gene3 Probe7 Gene3 ....... If I use "lmFit" in LIMMA package to fit the linear mode, there is a problem because I can not define single "ndups", I'm not sure if I can still use this

Microarray limma Microarray limma

updated 17.5 years ago • Yi Zou

div class="preformatted">Hi, I am using limma. Here is a error I met SubM is a 19k by 6 matrix > design [1] 1 1 1 -1 -1 -1 > PMAfit<-lmFit(subM,design,ndups=2,spacing=1,correlation

limma limma

updated 21.8 years ago • pingzhao Hu

which explains in a manner a non statistician might understand the difference between an analysis by limma and paired t-tests and SAM. We have now done all three and are trying to decide which analysis to give most weight to (our

limma limma

updated 21.7 years ago • Simon Kidd

<div class="preformatted">Hi , I have been trying to use limma to construct linear model of my normalized affymetrix data, but the program gives me an error at the last step of the calculation...div class="preformatted">Hi , I have been trying to use limma to construct linear model of my normalized affymetrix data, but the program gives me an error at the last step of the

limma limma

updated 22.1 years ago • Amin Momin

<div class="preformatted">Hi all, I've been using limma with Agilent data. By following the user guide, I could make MA plot with color based on information of the Spot Types File...div class="preformatted">Hi all, I've been using limma with Agilent data. By following the user guide, I could make MA plot with color based on information of the Spot Types...can ?t give the color to the M…

limma convert limma convert

updated 21.0 years ago • 宮本真理

div class="preformatted">Dear all, I am wondering what would be the optimal approach for limma to the following setup: I have an experiment repeated three times (A, B, C). Each repeat is measured at five different time...I want to see genes that are differentially expressed relative to T1. How do I do it correctly in limma? Best regards, j. -- -------- Dr. January Weiner 3 ----------------…

limma limma

updated 15.2 years ago • January Weiner

div class="preformatted">Hi all, I'm wondernig about what is the more relevant package among limma and Beadarray to analyse data from Illumina beadchip microarrays? Thank you for any feedback Leon [[alternative HTML

limma limma

updated 16.5 years ago • Leo Nitsche

div class="preformatted">Dear all, I am analyzing an RNA-seq experiment with voom+limma. The design of the experiment had two fixed effect factors that I combined into one vector including all combinations...of the levels of the 2 factors (as explained in the limma user guide, section 9.5), and a random effect that I model using the block and correlation arguments in lmFit. I am wondering

Genetics limma Genetics limma

updated 11.6 years ago • Julien Roux

<div class="preformatted">I am analyzing a 2-factor factorial Affy experiment, with 3 d.f. for each factor. I would like to get the F-tests for the main effects and interactions using limma. I have computed all the contrasts, and got the t-tests (both unadjusted and eBayes). I do know how to combine these into F-tests "by hand" but I could not figure out if there was a simple way to do t…

affy limma affy limma

updated 21.0 years ago • Naomi Altman

<div class="preformatted">hello, If we have many samples to be compared in an microarray experiment, for example, tissueType1 tissueType2 tissueType3 age1 4 4 4 age2 4 4 4 age3 4 4 4 each kind of sample has 4 biological replicates, primary interest are differential expression among…

Microarray limma Microarray limma

updated 20.8 years ago • Ren Na

I am having trouble reading the Agilent arabidopsis 22575 gene array using read.maimage in Limma under R 2.1.1 (I don't know the limma version, but I just downloaded using the R packages interface, and also used the update

Annotation limma Annotation limma

updated 20.5 years ago • Naomi Altman

div class="preformatted">Hi Briefly, I am using R 2.0.1 and limma 1.8.6. I have a double dye-flip experiment with only four arrays, and my targets and design matrix is so: > targets SlideName...Have I done something wrong (it is just after Christmas)? Is my data seriously screwed, or is my limma/R seriously screwed? Has anyone seen this before? Cheers Mick</div

limma limma

updated 21.0 years ago • michael watson IAH-C

a one-way ANOVA with 6 treatments, 2 replicates per treatment. We ran both SAM (excel version) and limma, and had very good agreement between them in terms of ranking the genes by the test statistic. For any set of the top K genes...of non-differentially expressing genes). I used the Bioconductor package "qvalue" to convert the limma p-values to q-values. Both routines are supposed to be base…

affy limma convert affy limma convert

updated 21.6 years ago • Naomi Altman

mathematical and technical description of the components in given in Sections 10.1 and 10.2 of the Limma User's Guide. Best wishes Gordon > Date: Tue, 3 Feb 2009 13:01:36 -0800 > From: "Sally" <sagoldes at="" shaw.ca=""> > Subject: [BioC] Limma...sagoldes at="" shaw.ca=""> > Content-Type: text/plain > > Hello, > > I have used Limm…

Preprocessing limma Preprocessing limma

updated 16.9 years ago • Gordon Smyth

gt;Dear Dr. Smyth and Bioconductor members: > >I have a question about M Values in toptable in LIMMA package. I know the >M in toptable is not a simple average from all the replicates, it is a >coefficient value from lmFit...1.441473, but it seems out of my >limmit. Could you help me to explain how this happens? How dose LIMMA >calculate the M in toptabl…

limma DOSE limma DOSE

updated 20.9 years ago • Gordon Smyth

The simplest way to handle this is probably to take the difference of the pairs and feed that into limma as a 1-sample t. --Naomi At 12:22 PM 4/20/2004 +1000, Gordon Smyth wrote: >At 03:09 AM 20/04/2004, Danielle Fletcher wrote: >>Hi...gt;> >>I am using limma to analyse a 2-colour microarray experiment. There are 2 >>treatments and 4 repli…

Microarray limma Microarray limma

updated 21.6 years ago • Naomi Altman

class="preformatted">Dear Tiandao, Dealing with multiple gal files is very tricky, but possible. In limma, you need to read in the GPR files for each GAL file separately, identify control spots separately, and normalize separately...TEXT/PLAIN; charset=US-ASCII > >Hello, > >I am analyzing cDNA microarray data using limma. I generated the GAL file >using the …

Microarray Normalization limma Microarray Normalization limma

updated 18.3 years ago • Gordon Smyth

<div class="preformatted">Hi Bioconductor users, I am having trouble understanding how multiple-testing adjustment is done in limma (specifically the decideTest). I am really confused about the meaning between moderated F p-value and the adjusted p-value...Hi Bioconductor users, I am having trouble understanding how multiple-testing adjustment is done in limma (specifically the decideTest)…

limma limma

updated 20.0 years ago • echang4@life.uiuc.edu

using bwa-mem and circular RNA quantification using sailfish-circ. I saw some publications using limma to analyze such datasets. However, I am getting strange results using LIMMA. Here is an example that is highly significant...with limma with 39 samples. When inspecting this gene (see panel A), I noticed there were 12 samples that had zero counts (points were...many other examples of significan…

limma R edger

updated 6.8 years ago • tan_pei_fang

div class="preformatted">Hello, I'm new using LIMMA for the analysis of two color arrays. I have been following the user guide but I have questions regarding the meaning

limma limma

updated 18.9 years ago • Andres Gutierrez

preformatted"> Hi, I am analysing microarray experiments with two groups, and with 3/4 groups using limma. I am looking at differential methylation between, for example, two groups with 3 samples in each, which I can easily do

Microarray limma Microarray limma

updated 13.2 years ago • Guest User

Marcus, I haven't seen this problem myself. I've just tried running the Weaver case study in the limma User's Guide, and it still runs correctly for me, using either R 2.15.1 or R-devel on Windows. There weren't any changes to...that part of the limma code between R 2.14.1 and R 2.15.1, so the change you are seeing may be in the stats package. Best wishes Gordon ---------------- original...C…

Normalization limma Normalization limma

updated 13.3 years ago • Gordon Smyth

like is mixed Gaussian distribution - two normal distribution as some people suggested. I think limma's assumption is normal distribution. I was wondering if there is any way to fix the problem or to convert my data to normal...distribution before applying to limma. Thanks, Jiang -- output of sessionInfo(): see question -- Sent via the guest posting facility at bioconductor.org. </div

limma convert limma convert

updated 12.1 years ago • Guest User

and put 20 control spot out of 360 total features in a single slide. I'd like to know whether limma has a normalization function that uses control spots. If yes, how to define control spots in limma? If no, is there any other

Microarray Normalization limma Microarray Normalization limma

updated 21.4 years ago • Sek Won Kong, M.D

div class="preformatted">Hi, I am using Limma to get differential expressed genes between case and control samples. In addition, I want to adjust the "weight" of patients...I got the error message :Error in qr.default(x) : NA/NaN/Inf in foreign function call (arg 1). Can limma handle the missing value in design matrix or I have to remove this sample ? Thanks, Chen [[alternative HT…

limma limma

updated 13.8 years ago • yao chen

class="preformatted">Dear List & Gordon, Firstly thanks to you and your team for the wonderful limma package and its well dcoumented manual. I have used it earlier for analysing both one colored and two colored data. But...with one of the datasets, I get the following warning with lmFit command in limma package. > fit <- lmFit(gset38932, design38932) Warning message: Pa…

Microarray limma Microarray limma

updated 11.4 years ago • Guest User

24 +0100 > From: Georg Otto <georg.otto at="" tuebingen.mpg.de=""> > Subject: [BioC] error in limma read.maimages(files, source="imagene") > To: bioconductor at stat.math.ethz.ch > > Hi, > > I am working with two-colour...data generated by Imagene image > analysis. I encountered a problem in limma 2.4.9 > > I try to read …

limma limma

updated 19.9 years ago • Gordon Smyth

div class="preformatted">Dear BioConductor list: I started to learn limma function for giving weight to all Genepix flags less than -50. Also I tried to filter out spots that, for example, show the

limma limma

updated 20.4 years ago • Jianping Jin

<div class="preformatted">Hi, I am analysing single-channel miRNA microarray data: I have 4 treatments at 4 time points, mostly in triplicate, spread approximately evenly across 2 batches. Previously I have used ComBat to reduce batch effects and then used Limma and AgiMicroRna to get DE miRNAs. However, I read on the list somewhere that it is better to add Batch as a factor to the model…

miRNA Microarray limma PROcess AgiMicroRna miRNA Microarray limma PROcess AgiMicroRna

updated 14.5 years ago • Segal, Corrinne

I know that for limma we use the following for when we have 2 control and 2 treated design <- model.matrix(~c(rep(0,2),rep(1,2))) and for Deseq2 condition...c("Control","Control","Treated","Treated"))   Now I have this questions one specifically for limma  1- does it matter in limma which design I use? for example if I have the frirst …

limma

updated 7.9 years ago • Bioinformatics

Hi, Im currently using limma to analyse methylation array data. The typical workflow is: ```r set.seed(12345) fit <- lmFit(methylation_data, design...Hi, Im currently using limma to analyse methylation array data. The typical workflow is: ```r set.seed(12345) fit <- lmFit(methylation_data, design, method...robust") fit_2 <- eBayes(fit) table &am…

limma methylation MethylationArray

updated 3.7 years ago • fluentin44

2007 17:28:23 -0400 (EDT) >From: Brooke LaFlamme <bal44 at="" cornell.edu=""> >Subject: [BioC] limma questions (normalization) >To: bioconductor at stat.math.ethz.ch > >Hi, I am very new to bioconductor and microarray...in >general. I am using Windows XP and R version 2.5.1. > >I have a few questions about the limma package that I am u…

Microarray Normalization probe limma Microarray Normalization probe limma

updated 18.3 years ago • Gordon Smyth

before and after treatment from the same mouse) and different treatments. I read the section in the limma user guide dealing with paired samples, but am not convinced that this is the best approach for my case. Would it be correct...to simply subtract the expression values after- before for each mouse and then use limma on these subtracted values to estimate the effect of the treatment? Many th…

limma limma

updated 15.1 years ago • Klemens Vierlinger

div class="preformatted">Dear all, I have a limma/multtest question. I have performed what I think is the equivalent of a t-test (of course, moderated) in limma below. Compare...and output are below. We have the same samples hybridized on two-color arrays, also analyzed with limma, with p-values in mt.maxT and limma that agree with the mt.maxT result from below, so I think there are differe…

multtest limma multtest limma

updated 21.6 years ago • Sean Davis

<div class="preformatted">Hi there, I have another question regarding limma and doing a block design on paired samples. this is how I understand this design to work, maybe someone can tell me If I got...div class="preformatted">Hi there, I have another question regarding limma and doing a block design on paired samples. this is how I understand this design to work, maybe someone can tell…

limma limma

updated 18.2 years ago • Mayra Eduardoff

div class="preformatted">Hi to everybody I have used limma to find out genes with different expression with high level of confidence in a Multiclass comaparison. Now I need to...separate different classes comparing for example sM vs UM. Have you any suggestions for visualizing limma results with heatmap?Is it incorrect to expect a separation of classes by heatmap with limma selected genes? …

Visualization limma Visualization limma

updated 20.0 years ago • daniela.marconi@libero.it

Kripa, Short answer: If you really must average over multiple probes for a given gene, then the limma function you are looking for is avereps(). Longer answer: This question has come up a few times recently on this mailing...step is done by the Illumina Genome Studio software, so has already been completed before entry into limma. On the other hand, summarizing multiple probes for a given ge…

probe affy limma beadarray probe affy limma beadarray

updated 13.8 years ago • Gordon Smyth

GSE1849-GPL96_series_matrix.txt.gz') i make the design and after that i make analysis with limma : library(limma) fit <- lmFit(exprs(gse), design) contrast.matrix <- makeContrasts(Normal_ACS = Normal - ACS , levels=design

limma limma

updated 11.7 years ago • Cherif Ben Hamda

to p-values... Is the topTable function using only 'p.adjust' to adjust the p.values? #R2.0.1, limma 1.8.13 fit<-eBayes(fit) #After applying eBayes, fit$p.value contains the p-values associated with the modified t-statistics

limma limma

updated 21.0 years ago • Giovanni Coppola

div class="preformatted">Hello, I've a question regarding the removeBatchEffect function in limma. I basically have a model expression_signal ~ organ + species + organ:species in which species can be considered a batch

limma limma

updated 12.4 years ago • arne.mueller@novartis.com

div class="preformatted"> Hi all, I am trying to load my agilent data to Limma using read.maimages function. Here's what I did: > library(limma)> targets<-readTargets("targets.txt")> RG <- read.maimages

limma limma

updated 14.1 years ago • Ella Chang

div class="preformatted">Hi, Dear Gordon: I tried to use limma to deal with ImaGene dataset I downloaded from ArrayExpress. I never deal with ImaGene data before and not familiar...and Cy3 signals are stored in two separate files for the same sample. I tried to read the data into limma and normalize them in the context of limma. and I keep running into issues and errors. and I wish you can he…

Normalization Cancer limma Normalization Cancer limma

updated 17.2 years ago • Ming YI [Contr]

<div class="preformatted">Dear Tina, limma handles random factors using the duplicateCorrelation() function -- see the User's Guide Section 8.2 for an example. It is admitedly an unusual method, but quite effective. Best wishes Gordon > Date: Mon, 14 Jul 2008 11:25:00 +0200 > From: Bettina Kulle Andreassen <b.k.andreassen at="" medisin.uio.no=""> > Subject: [B…

ExpressionData limma ExpressionData limma

updated 17.5 years ago • Gordon Smyth

Hello! I've got a small question regarding limma and couldn't find a direct answer anywhere: Does it make sense to perform limma on only a subset of genes? An example: I am...Hello! I've got a small question regarding limma and couldn't find a direct answer anywhere: Does it make sense to perform limma on only a subset of genes? An example: I am only interested in if there are differences in …

limma

updated 11.1 years ago • Simone

important points that need to be made here: 1. The moderated t-statistics and p-values returned by limma do not use any assumption about the proportion of DE genes. These statistics rank the genes in the same order as the B...discussion of how the prior proportion could be estimated but why this is not done automatically in limma. Smyth, G. K. (2004). Linear models and empirical Bayes methods f…

Microarray Genetics limma limmaGUI Microarray Genetics limma limmaGUI

updated 19.7 years ago • Gordon Smyth

div class="preformatted">Can i load my Imagene data output by Limma package? How? Thanks Dr. Cristian Taccioli Molecular Biology Unit Institute of Haematology and Medical Oncology "Ser

limma limma

updated 22.2 years ago • utepandragon@tiscali.it

preformatted"> >Wed Mar 23 19:48:20 CET 2005 >Hi BioC, > >For 3 experimental groups in LIMMA, when vennDiagram >is generated based on : > >mask <- c(1,1,1,2,2,3,3,3); >design <- model.matrix(~ -1+factor(mask)); >colnames...IDs: fit$genes[i,] >Is it possible to generate vennDiagram() for more than >3 gr…

limma limma

updated 20.8 years ago • Gordon Smyth

<div class="preformatted"> I wonder if somebody can tell me how I can use my P values from the limma test as input into topGo. This is what I tried: In topGo I usually do the following using the standard t-test: > geneList <- getPvalues(exprs(esetSub), classlabel = y, alternative = "two.sided", correction = "BH") > geneList[1:10] 1415670_at 1…

GO limma topGO GO limma topGO

updated 18.2 years ago • Caroline Reiff

<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

div class="preformatted">Dear Members, Is there any way to pre-filter the dataset in LIMMA before going on to differential expression analysis? I am using Agilent microarrays and would really like to filter...out genes/spots based on flags. Is this possible in LIMMA? Or is there any better way to filter than using flags in LIMMA? My dataset has a lot of genes and I really think I should use

limma limma

updated 13.8 years ago • Karthik K N

16 Dec 2005 21:06:57 -0500 > From: Naomi Altman <naomi at="" stat.psu.edu=""> > Subject: [BioC] limma - RG.MA > To: bioconductor at stat.math.ethz.ch > > Shouldn't RG.MA be: > > function (object) > { > object$R <- 2^((object

limma limma

updated 20.1 years ago • Gordon Smyth

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