Bioconductor Forum

I have a question based off the edgeR handbook.  I <span style="line-height:1.6">In the hand handbook it explains setting up contrasts as follows:</span> <pre

edger

updated 8.9 years ago • ciera.martinez

From the wonderful edgeR user manual (sections 3.3.1 p. 32 and section 3.3.3 p. 34) we find two different approaches: (1) each treatment is a different

edgeR limma

updated 8.6 years ago • Ekarl2

of defeats the purpose of the TagwiseDisp. Example code and sessionInfo: ################ library(edgeR) counts <- read.table("http://datos.langebio.cinvestav.mx/~cei/counts.tab") grp <- sub("_R.+", "", colnames(counts)) dge <- DGEList

updated 12.2 years ago • Cei Abreu-Goodger

Is it possible to combine all the counts from each BAM file and create an compatible table for edgeR? Thank you in advance &nbsp

edger htseqcounts

updated 7.0 years ago • mictadlo

I am asking a question relevant to this previous bioconductor-support question: https://support.bioconductor.org/p/71983/ I am wondering: is it better to perform edgeR-GLM on single cell data on the original counts or on normalized data, potentially normalized using scran?  For clarity, below is the pipeline I am currently planning to use. I am wondering if I should perform th…

edger scran

updated 8.1 years ago • amckenz

The results shows a big difference between the amount of differential bound regions identified with edgeR or DEseq2. What is the reason behind such difference? Which analysis method would best suit my type of study and why? Second

DESeq2 ChIPSeq DiffBind edgeR HistoneModification

updated 18 months ago • Giulia

to find a similar experimental design, I think it is most similar to *Section 3.4.2 Blocking* of the [edgeR user's guide](https://www.bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf), but

DESeq2 limma modelmatrix edgeR designmatrix

updated 2.9 years ago • rebecca.lea.johnston

perform differential expression (condition A vs B).    My specific question is if edgeR accept decimal / integer read counts for differential expression ?   Best regards Paddy

edger differential gene expression

updated 7.0 years ago • Padhmanand.Sudhakar

effect remove them from model and create simpler model for differential expression analysis using edgeR and DESeq2. Would you please let me know if there is a function in these packages to find the answer? &nbsp

edger deseq2 model matrix differential expression

updated 8.0 years ago • ta65

div class="preformatted">Hello! Thank you for the nice software and clear user guide. I am using EdgeR to analyse RNA-seq data. In the experiment there are several cell cultures with different knock-downs. The cell cultures

updated 10.4 years ago • Jussi Salmi

div class="preformatted">Dear all, I did a RNA-seq analysis two years ago (2011), using edgeR package (I do not remember the version). I was asked to analyze the data again, and now I am using edgeR_3.2.4. The comparison

edgeR edgeR

updated 11.1 years ago • Fernando Biase

Hello, I have a question about intercept and LogFC in edgeR. I am exactly following the article. [From reads to genes to pathways...the edgeR quasi-likelihood pipeline][1]. I also read

design.matrix logFC intercept edgeR model.matrix

updated 2.3 years ago • JK Kim

div class="preformatted"> I???m currently using EdgeR to analyze RNASeq data. I have one question of whether I have chosen the correct method for analyzing my multi-factorial

RNASeq edgeR RNASeq edgeR

updated 10.7 years ago • Guest User

time point within the same quality group Below is the detail of the analysis, which I used in edgeR. My question is, am I in the write track? How can I check whether the assumption of repeated measurments met or not? As you...time point within the same quality group Below is the detail of the analysis, which I used in edgeR. My question is, am I in the write track? How can I check whether the…

miRNA Normalization edgeR miRNA Normalization edgeR

updated 10.5 years ago • Guest User

right way and if not, how can I do this? Many thanks in advance! ``` >BiocManager::install("edgeR") >library(edgeR) #read in count data >countTable=read.table(file="count_matrix_TPM_metadata.txt",header=TRUE, row.names...Tissue7","Tissue8","Tissue9","Tissue10","Tissue10","Tissue10","Tissue11","Tissue12") >#create edgeR object using tissue type as groupin…

edgeR DifferentialExpression

updated 3.8 years ago • Christy

Hi there, I have an RNA-seq dataset from a polyploid species (consisting of sets of similar chromosomes, which consequently, contain highly similar paralogs). I'd like to know whether I could compare expression between these gene pairs using the aforementioned software. Is there a way to incorporate gene lengths in the detection of DEGs? I'm aware that you must supply raw data (although I'…

deseq2 edgeR normalization DGE

updated 4.9 years ago • grant.dejong

v10/n11/extref/nmeth.2645-S2.pdf, and looked at the difference of the TMM normalisation factors from edgeR and RLE from DESeq2 (recommended in the above). When the data is normalised there is good agreement on the mean expression

rnaseq single cell normalization edgeR deseq2

updated 8.1 years ago • kieranrcampbell

Hi seniors, I am using edgeR for Gene expression analysis, my data is time-course transcriptome but no biological replication. I also know that...Hi seniors, I am using edgeR for Gene expression analysis, my data is time-course transcriptome but no biological replication. I also know that there...The code is below: rm(list=ls()) setwd('H:/qde-2.20191220/DEG/') library("edge…

edgeR no replication glmLRT(fit coef=2)

updated 4.8 years ago • hong1ang

Hi, I am trying to do a pca plot for some gene expression data in R using edgeR. I have done a MDS plot but was hoping to do a pca. I have transformed my data into TPM to do this analysis. I have three wild

edger expression data pca

updated 4.0 years ago • waalkes

Cc: "'bioconductor at r-project.org'" <bioconductor at="" r-project.org=""> > Subject: Re: [BioC] edgeR: confusing BCV plot > > Dear Jim, > > Regarding the BCV plots, what I did not understand was the strange profile (at least

updated 12.0 years ago • Gordon Smyth

Hi, I am carrying out a multifactorial analysis on edgeR according to the experimental design shown at the end of this message (which I called design.all). My reference genotype

edgeR

updated 21 months ago • David R

I got the raw count and FPKM value. I used raw count for doing differential expression analysis by edgeR software, say, I compared A-B library. I found that among DEG genes reported by edgeR software, some few genes with positive

edgeR logFC FPKM

updated 8.0 years ago • Sara

Hello, I am trying to run a differential analysis with EdgeR for 2 RNAseq samples, with only one condition (1 treatment, 1 control), and I only have 1 replicate of each, which I know is...Hello, I am trying to run a differential analysis with EdgeR for 2 RNAseq samples, with only one condition (1 treatment, 1 control), and I only have 1 replicate of each, which I know is far

edgeR

updated 3.9 years ago • bertb

Hello edgeR support team, First off, thank you for the incredibly useful and well-documented package. It has been a great help for...Hello edgeR support team, First off, thank you for the incredibly useful and well-documented package. It has been a great help for our...species equally within its group? 2. If this is a valid approach is there a more natural way within edgeR to define the …

edgeR

updated 3.3 years ago • David

plot in the profile plot MAX_SITES = 1000 # Method to perform differential analysis; deseq2 or edger MOD = "edger" #if (MOD=="deseq2") { method=DBA_DESEQ2 } if (MOD=="edger") { method=DBA_EDGER } # Counts Object; Takes time to compute in single...Normalize by library size counts_norm <- dba.normalize(counts) # Normalize by the DESeq2 or EdgeR counts_norm <- dba.nor…

DiffBind

updated 8 months ago • Aswathy

div class="preformatted">i have two group of samples, each group have 3 biological replicate library(edgeR) library(limma) raw.data <- read.table("111",row.names=1) d <- raw.data[, 1:dim(raw.data)[2]-1 group <- factor(c(rep("sap", 3),rep("vas

updated 12.6 years ago • wang peter

I analyse my current RNAseq data set (two groups; each group with two replicates) using classic edgeR. I see couple strange results that i am trying to make sense of. I really appreciate any help from the list. 1) after filtering

RNASeq Normalization edgeR RNASeq Normalization edgeR

updated 12.3 years ago • gowtham

Hi All, I was wondering if you could look over my R code for differential gene expression using EdgeR. I am looking to determine differential gene expression between wild type (WT) cells and knockout cells (KO). Three biological...gene expression between WT and KO? Am I doing anything invalid with this code? <pre> library("edgeR") library("gdata") library("heatmaply") library("ggplot2…

edger rnaseq

updated 5.9 years ago • joseph.landry

1) Mapping the reads back separetely for all samples to assembled transcriptome (300k ) and used edgeR to call differential expression. I used the downstream processing pipeline mentioned in trinity which uses edgeR...got all vs all comparisons. I wanted to get expression profiling of those different stages. But with edgeR, i might not get good profiling as it is at sample level as you see that f…

edgeR edgeR

updated 11.7 years ago • empyrean999

I have conducted an analysis differential expression analysis using edgeR, but am receiving some criticism of the design of the statistical tests.  I am hoping someone can either verify that...between the populations across all food sources  Following the recommendations in the edgeR documentation (as I understood them in section 3.3.1), I set this up so that each treatment com…

edger limma

updated 9.4 years ago • jbono

class="preformatted"> Hi, I have done differential expression analysis over RNA-seq data using both edgeR and DESeq. There are some recently published studies which suggest TMM as the most efficient normalization method...along with DESeq normalization).edgeR already uses TMM. I wanted to ask do you think it is meaningful if I first normalized my raw data using TMM method and send...and of cou…

Normalization edgeR DESeq Normalization edgeR DESeq

updated 11.3 years ago • Guest User

<div class="preformatted"> Is it possible to adopt the CQN normalization method (Hansen, 2012) as an option of the edgeR function 'calcNormFactors' ? And the new shrinkage estimator for dispersion (Wu, 2012) that seems to be better than the currently...Is it possible to adopt the CQN normalization method (Hansen, 2012) as an option of the edgeR function 'calcNormFactors' ? And the new shrin…

Normalization edgeR cqn Normalization edgeR cqn

updated 11.8 years ago • Guest User

Hi, I folled this [instructions](https://f1000research.com/articles/5-1438/v2) but I got the bellow error: > logCPM <- cpm(y, prior.count=2, log=TRUE) > head(y$genes) genes 3 sp0025247 4 sp0025250 5 sp0025268 6 sp0025270 8 sp0025282 12 sp0056834 > y$samples...f1000research.com/articles/5-1438/v2) but I got t…

edger

updated 7.0 years ago • mictadlo

mod ``): <pre> dge <- DGEList(EM) dge <- calcNormFactors(dge) v <- cpm(dge, log=TRUE, prior.count=3) fit <- lmFit(v, design=mod) eb <- eBayes(fit, trend=TRUE, robust=TRUE) decideTests(eb) topTable(eb) ...</pre> How would this

limma-trend duplicatecorrelation arrayweights limma

updated 7.0 years ago • maltethodberg

I'm using edgeR to do differentially expressed genes analysis. Here's part of my code: <pre> fit <- glmFit(y, design) # conduct likelihood...I'm using edgeR to do differentially expressed genes analysis. Here's part of my code: <pre> fit <- glmFit(y, design) # conduct likelihood ratio

edger

updated 6.9 years ago • zhxiaokang

NextSeq 500, and they are 75 bp reads at ~32 million per sample.  We are following closely the EdgeR approach to finding batch effects given in the June 2016 version of the manual, including the TMM normalization.&nbsp

edger rnaseq batch effect read length

updated 7.9 years ago • Spollen, William G.

Dear Xiaohui, I suspect you mean more than 2 groups or conditions rather than 2 samples. edgeR already handles any number of groups. If you want to find genes highly expressed in one condition but not in the others...surely you need to make pairwise comparisons between the conditions, and that is exactly what edgeR does. In the next month, we will be adding linear model capabilities to edgeR, …

edgeR DESeq edgeR DESeq

updated 14.1 years ago • Gordon Smyth

4,6 and 8 days) with 7 replicates per data point (except t6 with 6 replicates). I am analyzing using EdgeR to identify differential expressed genes. I have used the following EdgeR script in my analysis: 1) I created the DGEList

edger Time series analysis

updated 4.0 years ago • josmantorres

Dear Bioconductor, I am currently performing an RNAseq analysis on rat samples using edgeR. Data was aligned using STAR against the rat genome (Rnor v6.0) and the genes were counted using featureCounts against...an approach similar to example "3.3 Experiments with all combinations of multiple factors" from the edgeR manual. #Prepare DGEList object > dgList <- DGELis…

edger glmqlftest()

updated 6.7 years ago • Andy91

Hi everyone. I have a question on using edgeR to analyze time series data. How to choose the degree of freedom when making design matrix? I basically follow the manual

edger

updated 4.3 years ago • Ruixuan

div class="preformatted">I am running the new EdgeR package 1.8 and have updated R to 1.12.0 and updated all the packages I have installed. I have an RNAseq experiment with

RNASeq edgeR RNASeq edgeR

updated 13.9 years ago • josquin.tibbits@dpi.vic.gov.au

I have an experiment where each sample is measured multiple times and samples are nested within the experimental group. I have noticed that my choice of sample reference level seems to influence the results. Below is a minimal example to show what I mean: <pre> library(edgeR) counts <- matrix(c(6,2,6,21,19,15,17,18,20,12), nrow = 1) counts <- rbind(counts, 25 - counts) …

edgeR model.matrix nested design reference group

updated 6.4 years ago • ri.lars

Hello all! Novice edgeR user here. I am analyzing RNAseq data using individual files for each sample (output from RNA star; tabular files with

edgeR

updated 7 months ago • aa.machado001

<div class="preformatted">Dear colleagues: I am using edgeR to examine differential expression on small RNA data I noticed this problem also when working with SAGE datasets: when...div class="preformatted">Dear colleagues: I am using edgeR to examine differential expression on small RNA data I noticed this problem also when working with SAGE datasets

SAGE edgeR SAGE edgeR

updated 12.4 years ago • alessandro.guffanti@genomnia.com

than a code issue. I have performed differential analyses of RNA seq data using the GLM approach in EdgeR. I have the following setup in an experiment using small worms: 4 treatments of a 2 x 2 factorial design: Treatment 1: high...in a nicer way), and I'm just wondering about the stats here. Best, Elise S. library(edgeR) genecounts <- read.delim("Trinity_genes_all.isoform.c…

edger

updated 4.5 years ago • elise.skottene

Hi folks, I know that to "run edgeR without replication" has been a popular question, but I'd like to specify the situation I'm in. I'd like to compare DGE from

edgeR StatisticalMethod

updated 3.0 years ago • Field -Ye

after the fold-changes but I feel like a more integrated solution is possible. I think that DESeq/edgeR can be adapted to integrate a gene-wise correction method. I know this is currently being addressed my multiple people

crispr edger deseq deseq2

updated 6.9 years ago • emanuelvgoncalves

Hello, I am performing DEG using edgeR. I am trying to design a matrix so that I can make comparisons control versus treated at different time points taking

edger

updated 5.5 years ago • adhikb

<div class="preformatted"> Hi, I am a graduate student at POSTECH and I ran into some troubles while running edgeR program. Currently I have six Chip-Seq samples, all of different condition. There are no biological replicate and no control sample. So when I try to run edgeR, it does not run for there is no biological replicate used for statistical testing. I wonder if there is a way to exp…

edgeR edgeR

updated 11.6 years ago • Guest User

<div class="preformatted"> I was using DESeq (and edgeR) for differentially expression analysis. In my current dataset I compare 3 biological replicates of control vs. 3 biol. replicates from a mutant. The resulting 4 top genes according adjusted pvalue by DESeq and edgeR have a very high variance. (The reason for this is, that this are genes located on the chrY and only one replicate of t…

edgeR DESeq edgeR DESeq

updated 12.8 years ago • Steffen Priebe

why Deseq probably isn't appropriate to use anymore, but I don't understand why Deseq2 and EdgeR are giving such different numbers of DEGs. Below is the code for Deseq. This results in 146 DEGs: total\_counts<-read.table...OQ\_YQ, "Results.csv", row.names=TRUE) \#End Deseq2 examples Below is the code I have used for EdgeR. This results in 15 DEGs: \#Start edgeR example x <…

edger deseq deseq2

updated 7.3 years ago • michael.steffen

<div class="preformatted">Hello, I'm using R/edgeR to analyze a 3x2 factorial RNA-Seq experiment and I would very much appreciate your help in specifying some contrasts. The design of my experiment has two factors, strain and treatment. There are three strains (A, B and C) and two treatments (Unstimulated and Stimulated). I have four biological replicates (except for one sample group whe…

updated 12.8 years ago • Benjamin King

I am new to edgeR and am trying to create a design matrix for my dataset. I have read the manual and many discussion threads, but cant find

egdeR design matrix batch effect

updated 4.9 years ago • ahsindoomilup

pre> Hi All,</pre> I am using edgeR to analyze data from my RNA-Seq time course (4 time points) experiment. This is my experimental design. It is a factorial...and fit negative binomial GLM and conduct likelihood ratio test. The following is my code using EdgeR package: <pre> library(edgeR) #The following is the count data year<-read.csv("C:/berryallsamplestotalexo…

edger edgeR main and interaction effects edgeR post hoc test

updated 8.9 years ago • padmaswami15

to identify differential expressed genes between two age groups. I am reading the user guide for the EdgeR program and found that it takes integer count data as input. however, the level 3 TCGA data are in the following format...count.</td> <td> <p> </p> <p> </p> </td> <td> <p> </p> <p> </p>…

EdgeR TCGA normalized count

updated 9.5 years ago • ycding

Hi,  I have two questions about EdgeR pipeline. I am dealing with no replicate situation and have two conditions to check the differential expression. I...Hi,  I have two questions about EdgeR pipeline. I am dealing with no replicate situation and have two conditions to check the differential expression. I am

EdgeR data.frame glmLRT

updated 9.1 years ago • amoltej

<div class="preformatted"> Hi, I am trying to analyze RNA-Seq data for (gene-level) differential expression between treatments, in a design incorporating multiple factors (effects of species * treatment & interaction, 4 replicates for each combination). I have reads that map to multiple locations (Single-End data) and while I'd first used Bowtie2/Tophat >> htseq (disca…

GO baySeq GO baySeq

updated 11.6 years ago • Guest User

div class="preformatted"> Hi, I am trying to use edgeR to compute differential gene expression. I have a quite simple experimental design: labExpId Patient sex Treatment

edgeR edgeR

updated 11.5 years ago • Guest User

as number of samples..) but it is an unqiue situation between my many SAGE experiments analyzed with edgeR.. Kind regards, Alessandro -- -- Alessandro Guffanti - Head, Bioinformatics, Genomnia srl Via Nerviano, 31 - 20020 Lainate, Milano

SAGE Regression edgeR BRAIN SAGE Regression edgeR BRAIN

updated 12.2 years ago • alessandro.guffanti@genomnia.com

fit <- glmFit(y, design) #Additions for clustering: logCPM <- cpm(y, log = T, prior.count = 3) noPatient <- removeBatchEffect(logCPM, design = model.matrix(~Disease+Disease:Treatment), batch = ??)</pre> The design

edgeR removeBatchEffect nested design

updated 7.9 years ago • Jenny Drnevich