Bioconductor Forum

gt; Subject: [BioC] TMM and calcNormFactors: Normalization in baySeq to > match edgeR and DESeq > > Hello, > I'm working on a couple analyses (currently pairwise) for 3'-DGE. Using > baySeq, edgeR, and DESeq are...of bayesian vs. exact-type statistics. I saw that baySeq's function > "getLibsizes" can use the edgeR implementation of TMM, but when …

Normalization Bayesian edgeR baySeq DESeq Normalization Bayesian edgeR baySeq DESeq

updated 12.8 years ago • Gordon Smyth

div class="preformatted">Dear edgeR developers and users, Just started using edgeR with next generation sequence (count) data. When calculating alpha, I am

edgeR edgeR

updated 16.0 years ago • Milena Gongora

Thanks to new C code from Aaron Lun, I have now committed a fixed version of goodTuring() to edgeR on the BioC devel repository. Best wishes Gordon --------------------------------------------- Professor Gordon K Smyth, Bioinformatics Division, Walter and Eliza...gt; > I'll see if I can find the bug or just work around it. > > I'm not actually using edgeR in this case other…

Category edgeR Category edgeR

updated 12.0 years ago • Gordon Smyth

Hi all,     I am using edgeR for Gene expression analysis. My question is about unequal no.of replicate. If we have 4 replicate of Control and 1 Case...Sample then is it fair to do analysis or we should go with edgeR without replicate like 1 case and 1 Control

edgeR replicate

updated 7.9 years ago • Sushant Pawar

<div class="preformatted">Hi All, I have an experiment that is exactly the same as the one described in section 3.5 (Comparisons Both Between and Within Subjects) in the manual<http: bioc="" doc="" edg="" edgerusersguide.pdf="" er="" inst="" packages="" release="" vignettes="" www.bioconductor.org=""> : The experiment has 18 RNA samples collected from 9 subjects. The samples correspo…

edgeR edgeR

updated 10.5 years ago • Son Pham

div class="preformatted">Hi List, I am analyzing my RNA-Seq data with edgeR. The next is my experimental design: d.GLM An object of class "DGEList" $samples group lib.size norm.factors R4.Hot HotAdaptedHot...expression variance of the corresponding gene (i.e., biological variation), as I understood from the edgeR manual. Am I correct? I tried to calculate it like this…

edgeR edgeR

updated 12.7 years ago • Miguel Gallach

div class="preformatted">Dear list, I have a questing regarding the 'plotMDS' function in EdgeR (and limma). In my case the plot generated (see attachment) is hard to read, since some of the labels are at the exact same place

edgeR edgeR

updated 12.1 years ago • Kaat De Cremer

t_2.1 = 100 reads.* * 2.2) Life stage 2, his transcript gets t_2.2 = 50 reads.* * * *Let's say edgeR being applied to the two 1) conditions produces:* * * *log2(t_1.1/t_1.2) = log2(4/2) = 1 with adjP = 0.5, meaning, it seems like* *the transcript...gt; Best wishes* *> Gordon* *>* *>>* *>> Hi Everyone,* *>> I have been using edgeR for the…

RNASeq GO Cancer limma edgeR RNASeq GO Cancer limma edgeR

updated 11.4 years ago • Alvaro J. González

Hello list I would like to calculate standardized effect size in edgeR, I found this post https://www.biostars.org/p/140976/ for DEseq2 Is the formula below the right calculation also...Hello list I would like to calculate standardized effect size in edgeR, I found this post https://www.biostars.org/p/140976/ for DEseq2 Is the formula below the right calcul…

edger effect size cohen d

updated 5.9 years ago • mali salmon

div class="preformatted">Hi, I am running edgeR on 6 RNAseq samples that were generated using the exact same protocol but are from different Illumina project runs...In theory, no genes should be differentially expressed. Nevertheless, edgeR identifies almost 7,000 genes as DE at a FDR rate of 0.1. This is very puzzling. I ran edgeR using the classic approach (exactTest...Could there anything…

Sequencing RNASeq edgeR Sequencing RNASeq edgeR

updated 10.7 years ago • Blum, Charles

div class="preformatted">Hi all, I am trying to compare limma (with voom) and edgeR for RNA-seq differential expression analysis, and I have noticed that while edgeR's glm functionality closely matches...same data with two equivalent design matrices, one with an intercept term and one without: library(edgeR) dge <- DGEList(...) # Imagine data here sampledata <- data.frame(timep…

limma edgeR limma edgeR

updated 11.8 years ago • Ryan C. Thompson

<div class="preformatted"> I was wondering whether I could use EdgeR to test for differences between two groups with an inherent bias in their reads proportional to each other. By this I mean that instead of each gene being tested with the null of 1:1 could I modify edgeR to test for a gene where the null is say 1.5:1 and another gene with a null of 3:4 etc. Many thanks in advance, Emily…

edgeR edgeR

updated 10.7 years ago • Guest User

<div class="preformatted"> Hi! it would be of great help, if someone could suggest a solution to the following problem. I used edgeR to analyze RNA Seq expression data (3 different cell lineages with 2 biological replicates for each lineage). I used the plotMDS () function to get a 2D plot of multidimensional scaling. I was asked to perform a 3D plot but I am not able to find a solution A…

edgeR edgeR

updated 10.8 years ago • Paraskevas Iatropoulos

do a very good job guiding the users on how to format their data as to import it into DESeq2 and edgeR. At the end of the tximport edgeR part of the vignette the authors state: 'y <- y[keep, ] y is now ready for estimate dispersion...functions see edgeR User's Guide' As a consequence, I originally followed the edgeR vignette and estimateDisp(y, design=design), where design...glm fun…

edgeR tximport differential expression

updated 4.3 years ago • hollandademello

<div class="preformatted"> I am trying to run an EdgeR script that I have been using for several years. I am getting an error message early on in the script and cannot figure out what is wrong. Please advise. -- output of sessionInfo(): The downloaded binary packages are in /var/folders/Fx/FxdWG0DyE3eRfY72Zl3JxU+++TI/-Tmp-//RtmpoQbYDm/ downloaded_packages > library(limma…

edgeR edgeR

updated 10.5 years ago • Guest User

Dear Mark I cannot figure out how to specify which conditions to contrast against each other in an edgeR exactTest. I do the following: > library( edgeR ) > counts <- matrix( rnbinom( 600, 5, .1 ), ncol=6 ) > conds <- c( "A", "A", "B", "B", "C", "C" ) > dgl <- DGEList

edgeR edgeR

updated 14.8 years ago • Simon Anders

<div class="preformatted">Hello everyone, I thought of conducting a parallel DE analysis with EdgeR and DESeq using a dataset that I have been working on lately. The dataset has two conditions with two biological replicates each. Let's say: Wild Type, Wild Type, Knock Out, Knock Out. It's a smallRNA-Seq dataset, mapped to miRNAs. I have tried various analyses using both programs and I …

Normalization edgeR DESeq Normalization edgeR DESeq

updated 11.8 years ago • Ioannis Vlachos

data, I see that one could test for "differential efficiency" simply by using an interaction test in edgeR. However I have no experience of this type of analysis, and I don't know what is scientifically sensible. Making good plots...gets t_2.1 = 100 reads. 2.2) Life stage 2, his transcript gets t_2.2 = 50 reads. Let's say edgeR being applied to the two 1) conditions produces: log2(t_1.1/…

RNASeq GO limma edgeR RNASeq GO limma edgeR

updated 11.4 years ago • Gordon Smyth

<div class="preformatted">Dear EdgeR community, I am new to edgeR and still in the phase of reading the vignette in details to be able to use it for my data. I have a question in understanding the model.matrix. On page 27 (paragraph 3.3.2 "Nested interaction formulas"), the design is defined as: > targets Sample Treat Time 1 Sample1 Placebo 0h 2 Sample2 Placebo 0h 3 Sample3 Placebo …

RNASeq Cancer edgeR RNASeq Cancer edgeR

updated 10.6 years ago • Mike Miller

<div class="preformatted"> Hi, I have a question regarding the minimal number of genes that we can test in an analysis with edgeR. Let me explain, in a study, edgeR have been used for testing the differential expression of three viruses between two conditions, without considering the counts on other features. That is, the data frame d$counts has only three lines (and 4 columns, as there i…

Organism edgeR Organism edgeR

updated 11.9 years ago • Guest User

r-project.org=""> >> Subject: [BioC] Please help! How to specify factors for a RCBD in >> edgeR >> >> Dear Tilahun, >> >> The first step is that you need to create a data frame containing the >> experimental...message ------------------- >> [BioC] Please help! How to specify f…

edgeR edgeR

updated 12.6 years ago • Gordon Smyth

333 I divided all the mapped transcript reads by 4 and then did the normalization and analysis With edgeR. What do you recommend to do with the 4th sample counts? Lana Schaffer Biostatistics, Informatics DNA Array Core Facility

edgeR edgeR

updated 12.9 years ago • Lana Schaffer

Seanchez and I'm a post-doc at the VUmc in Amsterdam. The reason of this e-mail is that im running edgeR in an expression dataset and getting the following error when calculating the GLM common dispersion: *Error in beta

edgeR edgeR

updated 12.0 years ago • Javier Simón-Sánchez

wrong. In fact, the output doesn't make sense to me. The CPM and average logCPM values output by edgeR should be unchanged regardless of the comparison you are testing, so the two output tables you give cannot be from the...list <bioconductor at="" r-project.org=""> > Cc: bioinfo at genomnia.com > Subject: [BioC] edgeR on ncRNA analysis question > > Der BioC ed…

Normalization edgeR Normalization edgeR

updated 10.8 years ago • Gordon Smyth

<div class="preformatted">Dear Zhe, To do clustering of RNA-seq profiles using the edgeR packages, you can use the plotMDS.dge function. See the User's Guide for examples. This function is already designed for...div class="preformatted">Dear Zhe, To do clustering of RNA-seq profiles using the edgeR packages, you can use the plotMDS.dge function. See the User's Guide for examples. T…

Normalization Clustering edgeR Normalization Clustering edgeR

updated 14.2 years ago • Gordon Smyth

<div class="preformatted">Dear all, I'm currently using edgeR to detect the differentially expressed genes from a RNAseq datasets, and I'm also using the gof() function to test for potential...div class="preformatted">Dear all, I'm currently using edgeR to detect the differentially expressed genes from a RNAseq datasets, and I'm also using the gof() function to test for

RNASeq edgeR RNASeq edgeR

updated 12.6 years ago • Yuan Tian

div class="preformatted">Dear all, I am using EdgeR on RNA-seq data for differential analysis. I would like to see the impact of the double normalizations (TMM + libsize) on

Normalization edgeR Normalization edgeR

updated 12.2 years ago • François RICHARD

for each independent contrast. This extension allows very general access to anova-type tests using edgeR. I committed this change to the official release of edgeR yesterday. Best wishes Gordon --------------------------------------------- Professor Gordon K Smyth, Bioinformatics...gt; > [BioC] Equivalent of contrasts.fit & multi-contrast decideTests for edgeR? > Ryan C. …

limma edgeR limma edgeR

updated 11.8 years ago • Gordon Smyth

Hello, I am a new user to EdgeR and am curious if there is a straightforward way to test for interaction significance in genes akin to anova. For example...factor2, reduced = ~factor1+factor2)` Can I do something similar with the `glmLRT` function in edgeR? Thank you very much

edgeR

updated 7 months ago • pl23

experiment I'm analyzing read counts on different sets of genomic intervals. I would like to apply edgeR functions to normalize read counts but... Since my sets of intervals do not necessarily overlap, I thought I can extract

edgeR edgeR

updated 11.6 years ago • Cittaro Davide

<div class="preformatted"> Dear friends, We are very interested in testing main effects and interactions for a 2x3 factorial RNA-seq project we have been running (we have reasonable replication: 7 biological replicates per treatment combination, i.e. 42 libraries in total). >From our reading of the edgeR Users guide and various posts on-line, it looks as though the package is set-u…

edgeR edgeR

updated 10.8 years ago • Guest User

div class="preformatted">No, the unbalanced sample numbers will not cause edgeR to give asymmetric DE results. Quite the opposite. Since, miRNA results are expected to be globally assymmetric, I would...expect edgeR to be under-stating rather than exaggerating the assymetry. BTW, please upgrade to the current release of R, Bioconductor...and edgeR. Best wishes Gordon On Tue, 30 Apr 2013, …

miRNA Cancer edgeR miRNA Cancer edgeR

updated 11.4 years ago • Gordon Smyth

gt; To: bioconductor at r-project.org, bioconductor-request at r-project.org > Subject: [BioC] edgeR - MDS plot > > Hello, > I am new to this kind of analysis in MDS plot. I used edgeR for DGE > analysis, which showed a great

edgeR edgeR

updated 13.5 years ago • Gordon Smyth

RNA-seq experiment with treatment and control, each with 3 biological repeats. I run my data through edgeR and obtained differentially expressed genes (DEGs). Due to the low sample number and small effect size, there are likely...shuffling the columns and generated 1000 permuted dataframes. Next, I run each dataframe through my edgeR pipeline, which produced results such as RowName, logFC, logCPM…

rna-seq edgeR

updated 5 months ago • Netanel

<div class="preformatted"> Dear edgeR users and developers, we used Solexa sequencing in order to detect RNase E processing sites. Therefor we splitted a RNA...div class="preformatted"> Dear edgeR users and developers, we used Solexa sequencing in order to detect RNase E processing sites. Therefor we splitted a...RNAs. So I want to ask, if it is appropiate to do a single nucleotide …

Sequencing Normalization edgeR Sequencing Normalization edgeR

updated 13.6 years ago • Jens Georg

div class="preformatted">Hello, I am interested in applying my edgeR results to a modulated modularity clustering algorithm to explore community structure in the significantly differentially

edgeR edgeR

updated 10.6 years ago • Laura Eierman

div class="preformatted">Hi everyone, I have been experimenting with using EdgeR with proteomics data (spectral counts for now). I was a little confused how the TMM normalization works on proteomics

Proteomics Normalization edgeR Proteomics Normalization edgeR

updated 10.7 years ago • Phinney, Brett

Hi Can anybody point out to a tutorial/paper which explains the normalization method used by edgeR? <span style="line-height:1.6">Another thing, though, TMM is the default normalization method of edgeR, can one specify, any...other normalization methods in edgeR?</span> <span style="line-height:1.6">Thank you!</span> <span style="line-height:1.6">Prerna</span

edger

updated 9.1 years ago • p_das

<div class="preformatted">Hi, 1) If you remove the calcNormFactors() function, there will be no normalization, which is not recommended in most cases. 2) To make a qq-plot for your Poisson data, the simplest way is as follows: design <- model.matrix(~group) fit <- glmFit(y, design=design, dispersion=0) gof(fit, plot=TRUE) 3) To make the same graph with a NB distribution us…

Normalization graph edgeR Normalization graph edgeR

updated 10.6 years ago • Yunshun Chen

1] package. This tutorial is [great][2] I have a paired design as described in section 3.4.1 in the [edgeR guide][3]. I have 4 independent subjects and each has a pre-treatment (control) and post-treatment sample. I want to see what...differential expressed in each subject after treatment. My base R code is as such: ```r library(edgeR) data=read.csv("~/Rmd_docs/transcriptome_counts.csv") data…

edgeR R tidyverse tidybulk

updated 22 months ago • Amit Indap

gets t_2.1 = 100 reads. 2.2) Life stage 2, his transcript gets t_2.2 = 50 reads. Let's say edgeR being applied to the two 1) conditions produces: log2(t_1.1/t_1.2) = log2(4/2) = 1 with adjP = 0.5, meaning, it seems like the transcript...gt; > Best wishes > Gordon > >> >> Hi Everyone, >> I have been using edgeR for the last coupl…

RNASeq limma edgeR RNASeq limma edgeR

updated 11.4 years ago • Alvaro J. González

<div class="preformatted">Dear Iain, I think you might be after an interaction plot, see ?interaction.plot I've never seen anyone do this for count data. However I guess you could make such a plot approximately in edgeR by computing lcpm <- log2(cpm(y)) Then using interaction.plot(x.factor, trace.factor, response=lcpm[i,]) where 'i' is the gene of interest. Best wish…

edgeR edgeR

updated 12.9 years ago • Gordon Smyth

for the 2.10 Bioconductor release is very close. There are a few packages that depend on or suggest edgeR. This email is to alert developers to changes in edgeR that might potentially break code. One of the changes below was

edgeR edgeR

updated 12.5 years ago • Gordon Smyth

div class="preformatted"> Hello dear List, I conducted an analysis with EdgeR and I thank you for this software. I have a list of DE genes after treatment A and one after treatment B. using the cntrast

edgeR edgeR

updated 11.9 years ago • Guest User

I am doing edgeR glmLRT() test because I don't have any replicates. I have three groups and I made the design as: design <- model.matrix...following section 3.5 of this [edgeRUsersGuide](https://bioconductor.org/packages/3.3/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf). But I am getting the same DE genes with opposite expression for groupR:treatmentM

edger design matrix glmlrt

updated 7.7 years ago • simarsidhu25

Hello Dears, I have questions and I want your kind help? I did gene filtering as below in edgeR which is exactly the same with my filtered genes in DESeq2 which I did before and I like that because I had a thought I...Hello Dears, I have questions and I want your kind help? I did gene filtering as below in edgeR which is exactly the same with my filtered genes in DESeq2 which I did before…

edger

updated 4.4 years ago • Do it!

div class="preformatted">I am using edgeR to analyze RNA-Seq data. This is my script: library("edgeR") ############################# #read in metadata & DGE ############################# composite_samples <- read.csv(file...shall contain the normalized counts for each sample in each condition. My understanding is also that edgeR adds pseudocounts BEFORE performing the library n…

edgeR edgeR

updated 10.1 years ago • Nick N

<div class="preformatted">Dear Daniela, edgeR can work with any design matrix. Just setup your interaction model using standard R model formula. See for example Chapter 11 of: http://cran.r-project.org/doc/manuals/R-intro.pdf Best wishes Gordon > Date: Mon, 29 Oct 2012 16:24:31 +0100 > From: Daniela Lopes Paim Pinto <d.lopespaimpinto at="" sssup.it=""> > …

Sequencing edgeR Sequencing edgeR

updated 11.9 years ago • Gordon Smyth

<div class="preformatted">Hello, I'm trying to use edgeR to analyze some RNA-seq time series data. I have four time points. The first and last time points have three replicates, while the middle two have two replicates. The following gives the error I get: require(edgeR) counts <- read.csv("http://www.duke.edu/~csm29/counts.csv",row.names=1) d <- DGEList(counts) d <- c…

edgeR edgeR

updated 13.6 years ago • Colin Maxwell

<div class="preformatted">Hi KJ Lim, Once you have your row names of interest i.e up-regulated or down- regulated genes you can easily fetch other information for those row names. For instance the results from limma link back to samples by heatmaps. A heat map of upregulated genes: >expVal<-(eset[geneList,]) # Assuming eset if the expression set, it will take all columns for r…

limma edgeR limma edgeR

updated 12.3 years ago • Ekta Jain

div class="preformatted">Hi all, I am looking for a bit of enlightenment regarding edgeR. We are applying edgeR using ANOVA-like testing. We have 2 conditions (Cases and Controls) sampled at 2 treatments (untreated

edgeR edgeR

updated 11.2 years ago • Michael Breen

<div class="preformatted">I have 2 questions about dispersion in edgeR. 1) The model implies that as sequencing depth increases, the power for testing differential expression comes to an asymptote...div class="preformatted">I have 2 questions about dispersion in edgeR. 1) The model implies that as sequencing depth increases, the power for testing differential expression comes to an

Sequencing edgeR Sequencing edgeR

updated 14.2 years ago • Naomi Altman

<div class="preformatted">Dear Bioconductor list, I am using edgeR to test for differential expression but I also I would like to know how to test whether expression variability (per gene...div class="preformatted">Dear Bioconductor list, I am using edgeR to test for differential expression but I also I would like to know how to test whether expression variability (per...to that obtain…

edgeR edgeR

updated 3.5 years ago • Miguel Gallach

step makes only a small difference to the final tagwise results. We are gradually revising all the edgeR code to make the classic and glm pipelines consistent with one another. In the latest versions of edgeR, you can simply...bioconductor at="" stat.math.ethz.ch=""> > Subject: [BioC] GLM common and trended dispersion EdgeR. > > Dear All, > > I have a query…

edgeR edgeR

updated 10.7 years ago • Gordon Smyth

treat them as replicates), then your experiment reduces to a simple two group problem, and the edgeR User Guide provides plenty of advice on how to do that. As the posting guide says, "Read the relevant R documentation". However...gt; To: bioconductor at r-project.org, robinmjelle at gmail.com > Subject: [BioC] DE in EdgeR > > > I am testing DE between two groups tha…

edgeR edgeR

updated 11.9 years ago • Gordon Smyth

I want to perform a GSEA on RNA-seq data, I use the filterbyexp() function in the DGELlist in edgeR. I am not sure about hte arguments I use : I would like to keep all genes with an expression of at least 10 cpm in 10% of samples

edgeR

updated 2.6 years ago • Simon.garinet

T2 and T3), could you please suggest how I can improve below code to extract pairwise comparisons in edgeR after importing data from phyloseq object to edgeR. dge = phyloseq_to_edgeR(kosticB, group="Treatment") # Perform binary

edger

updated 5.3 years ago • nabiyogesh

gt; raw counts as well as effective counts (after correction for > distribution biases). Since edgeR recommends using raw counts, I have > used these and obtained expected results for genes that pass a min. cpm > cutoff...eXpress developers recommend the use of rounded > effective counts over raw counts even for edgeR. As you already know, the edgeR developers recomme…

edgeR edgeR

updated 11.4 years ago • Gordon Smyth

Hi, i am using edgeR and i want to print the reads normalized with the TMM method but i have not found the command. Is there a command in edgeR

edger

updated 8.7 years ago • ribioinfo

Message: 24. Questiond about the descrepancy between edgeR and limma- voom (Ming Yi) Hi, Dear all: I am looking for advice for what I observed in my analysis results using the same data...but two very close related methods: limma-voom and edgeR. for purpose of consolidation and comparison, since I try to get as accurate DEGs lists for my next step downstream analysis...for the same dataset, I …

RNASeq edgeR RNASeq edgeR

updated 10.6 years ago • Yunshun Chen