Hi, I have used edgeR for single factor and two factor experiments, but I am confused with 3 factor experiments. my code looks like below:
<pre
updated 9.2 years ago • gthm
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Hi,
I have RNAseq data from an shRNA knockdown screening experiment and I 'm trying to perform differential test using EdgeR. What we are interesting in is the difference between control and treatment (Dox) at the last time point compared to the first time point. So my design matrix is as follow and I applied estimateGLMCommonDisp function with a robust option without giving a design ma…
updated 4.9 years ago • sirintra
encountered this problem? And I would like to know how to justify this case (statistical package edgeR calls it differential expressed, but it's clearly not -- visually).
Thanks.
SnowRu
 
div class="preformatted">Hi all,
i am analysing a two-factorial RNA-seq experiment using edgeR. The
design of my study has two factors, genotype and treatment.
Genotype has three levels (A,B,C), "treatment" has two levels...below:
#####################################################################
BEGIN CODE
library(edgeR)
# Generate a dataframe of neg.binom counts
set.seed(50)
s <-…
div class="preformatted">
I have a question about the edgeR package in R. I have a dataframe and
design matrix like below and every time i get the same error. Can
anyone help me with
genes between several breast cancer subtypes. To this end, I am using an ANOVA-like test from the edgeR package. I have several questions about it. The code looks like that:
```r
# The conditions as a factor
head(groups)
[1] Basal-like
Hi support team,
I'm an RNA-seq & edgeR beginner trying to wrap my head around whether/how to use blocking in my complex experimental setup. Thanks for...I need to be treating the prox/dist samples that come from the same flower as pairs**, like in the edgeR User's Guide examples where control and treatment samples come from the same patient. It's not quite the same scenario..…
Noticed a discrepancy in config file parameter names.
In all documentation, the DBA$config$edgeR$bTagwise and DBA$config$DESeq2$fitType parameters are structured as written here. However, in the actual DBA object
First, let me apologize in advance for posting a problem which might prove to be out of the scope of this forum.
I am currently analysing data from a RNA-seq experiment in bacteria:
The experiment involves 60 RNA samples, corresponding to two groups of bacterial strains (commensal (C) and disease-causing (D)); each group consisting of 15 different strains; either strain treated (IND) and not tr…
updated 9.6 years ago • Mauve
Hi,
I'm interested in performing some DE analysis using edgeR package. For this purpose, I've been following the manual and some other related older contributions made here (https
Hi there,
I have been using `edgeR` for quite some time now, and now I am facing with a question that applies to experimental designs that are not the "traditional
updated 13 months ago • lucap
pools.
My question now is how to do this properly.
We already had a look at the manual from edgeR (Chapter 2.12) and thought we could use the common dispersion estimated from the replicates for the pools. This would...have to be used for all genes, and we are not sure if this would be the best way.
```r
library(edgeR)
counts <- read.delim(data, header=T, row.names="ID")
group…
you are quite busy, but I cannot seem to locate this information online, on this forum and or on edger (when I google), if you could please help I would really appreciate it as I really want to use Deseq for this analysis.
[1]: https
i hava the RNAseq coutns data and fpkm data from TCGA, i want to know the fold change of tumor tissue RNAseq expression contrast of normal tissue RNAseq expression ,counts data is the RNA reads number, fpkm data is similar to real RNA expression. i found that the logFC results from DESeq2 and edgeR analyse using counts data are different from that i use mean tumor f…
Hello,
I am wondering what the correct way to define the design in the EdgeR workflow is for a pairwise analysis, while also accounting for batch effects, in terms of the design <- model.matrix
updated 9.6 years ago • cinderelliedoll
DESIGN))</pre>
We tried to do initial filtering based on CPM values as follows according to the edgeR Vignette.
keep<-rowSums(cpm(y)>1) >=5
y<-y\[keep, ,keep.lib.sizes=FALSE\]
Our intention was to filter CPM values per
updated 6.9 years ago • teshome.dagnem
Hi, I have a question about contrasts for more complex GLM models in edgeR.
Taking the section 3.5 example as a starting point
```
> targets <- data.frame(Disease = factor(rep(c("Healthy","Disease1...Hi, I have a question about contrasts for more complex GLM models in edgeR.
Taking the section 3.5 example as a starting point
```
> targets <- data.frame(…
differential expression (DE) analysis` to identify enriched peptides in a `phip-seq` analysis using `edgeR`. However, as there are no replicates available, I am uncertain about how to determine the reliability of the ***BCV (square
updated 17 months ago • f_rahmdani
Hi everyone! This is a bit long but I hope to state my problem more clearly
I've been trying to perform an analysis on the effects of a treatment over different time points using RNASeq with both limma and edgeR but I'm a bit confused with how to approach and interpret the results.
The experiment consists of samples taken at 5 different time points, with both treatment and control (thi…
updated 8.3 years ago • joelrome88
class="preformatted">Dear Ina,
voom is already quite robust as it is (more so than un-robustified
edgeR).
However limma also has special options for either observation or
dispersion outliers.
In the sequence
v <- voom(y,design...gt; Subject: Re: [BioC] tagwise parameters for negative binomial
> distribution in edgeR
>
> Hi Ina,
>
> I don't …
Hi I have a quick question about a paired samples and batch effect correction. Especially I am seeking a solution for edgeR or limma/voom.
A few days ago, I fount the following post.
https://support.bioconductor.org/p/92753/
In his case, subject and...question about a paired samples and batch effect correction. Especially I am seeking a solution for edgeR or limma/voom.
A few days ago, I foun…
updated 5.9 years ago • NGS-seeker
IN or OUT and hpi: 0,1,2,4 and 6h). Indeed, I am interested in the triple interaction, written on edgeR as:
((Bact.IN.Tx - MOCK.IN.Tx) – (Bact.IN.T0 - MOCK.IN.T0)) –
((Bact.OUT.Tx- MOCK.OUT.Tx) - (Bact.OUT.T0- MOCK.OUT.T0))
Now, I am
updated 6.2 years ago • David Rengel
nbsp; the RNAseq read counts data can do the different RNAseq expression by the DESeq2 and edgeR , but i also want to get the normalization gene expression data such as FPKM data ,and do the later clinical survival analysis...with gene expression. can i get the normalization gene expression by edgeR and DESeq2 data
Hi,
I am trying to replicate the case studies at the end of the edgeR user guide to verify a workflow I’ve developed. Particularly I am interested in the Pasilla knockdown study to test...Hi,
I am trying to replicate the case studies at the end of the edgeR user guide to verify a workflow I’ve developed. Particularly I am interested in the Pasilla knockdown study to test doing
updated 4.4 years ago • ali.sajid.imami
my name is Alex Martinez and I am currently a graduate student at Purdue University. I am using edgeR to conduct differential gene expression for a project wherein I'd like to compare 2 treatment groups (_control_ versus..._treatment_) across 3 population groups (_lm_, _lc_, and _ct_). After reading through the edgeR user guide, I decided to opt for the Blocking method (section …
I have a DGEGLM object from edgeR called fit2
<pre>
fit2 <- glmFit(counts(Data), design, disp2$tagwise.dispersion,offset=-offst(dataOffset))</pre>
 
updated 5.8 years ago • zoppoli pietro
span style="line-height:1.6">In EdgeR, the 'log cpm' values are calculated as:
</span><span style="line-height:1.6">log2(t( (t(x)+prior.count.scaled) / lib.size ))</span>
However
We use edgeR for its GLM fitting.
When we present lists of differentially-expressed genes, colleagues ask to see the raw expression
updated 8.2 years ago • david.hughes
Hello,
I am trying to use edgeR with a custom offset matrix (i.e., a different offset value in the GLM for each gene). I'm doing something like this:
 
updated 7.8 years ago • my4
from finding differentially
expressed genes and therefore I might not be using any other function
of
edgeR. To scale two libraries:
files =c('Lib1.txt','Lib2.txt')
data <- readDGE(files)
factors.TMM <- calcNormFactors(data,method
updated 10.8 years ago • Bade
i found the the p value and FDR are lower using exactTest than using glmQLFTest in edgeR when comparing two groups , I want to know why the results is very different between exactTest and glmQLFTest
updated 6.0 years ago • ZihaoXing
and no downregulated genes using lofFC 1.2 and FDR < 0.05.
I also used same data with edgeR.
<pre>
library(edgeR)
group <- factor(paste0(samples2$Type))
y <- DGEList(U2,group = group)
design2 <- model.matrix(~ 0 + group)
colnames...because it doesn't show any down regulated genes.
2) with deseq2 there are two upregulated and with edgeR there are four. A…
updated 6.3 years ago • Biologist
Hello everyone!
I have a large dataset of patients with Systemic Lupus Erythematosus (SLE) and Healthy Controls and I would like to perform various DE comparisons using edgeR, but I am having some doubt about my design matrices.
A little more info to better clarify the situation. SLE Patients in...Erythematosus (SLE) and Healthy Controls and I would like to perform various DE comparisons us…
updated 8 months ago • Geo
12</td>
<td>Treat</td>
<td>Knockdown</td>
</tr>
</tbody>
</table>
I am familiar enough with EdgeR to perform basic pairwise comparisons between these samples using an additive model. However I have been told I need...of the treatment and knockdown.
__Questions regarding ANOVA : __
1. I have read through the EdgeR manual, and I under…
updated 7.9 years ago • jjh
HI all
I am analyzing an RNAseq dataset to find DE genes using edgeR. Strangely I get no significantly differentially expressed genes, and the same FDR for every gene when summarizing...help would be appreciated to find out where I am going wrong, many thanks!
My Code:
<pre>
library(edgeR)
d <- DGEList(counts=data_matrix[2:46079,3:10], group=group)
d$samples
isexpr <- r…
Hello all,
I have a question concerning the calcNormFacotrs() in edgeR. There are three methods that I could choose from: "TMM", "RLE", and "upperquartile". I am wondering how could decide which one...gt; d <- DGEList(counts = counts, group = grp )
Then I calculated the normalization factor by edgeR:
> n <- calcNormFactors(d)
By default, this function uses the "TMM" met…
updated 10.0 years ago • Zhan Tianyu
Hi everyone,
<span style="line-height:1.6">I have a problem with edgeR right now, and I cannot figure out what the cause is.</span>
I use these commands:
<pre>
x <- read.delim("input.csv",row.names...lt;- c(1,1,2,2,3,3,1,1,4,4,5,5,1,1,6,6,7,7,8,8,9,9,10,10,11,11,12,13,13,14,14,15,15,16,16)
library("edgeR")
d <- DGEList(counts=x, group=group)
d$samples$lib.si…
updated 9.1 years ago • bastian.hornung
I have miRNA data and I am analyzing it for differential expression using edgeR.
The data consists of four different groups (A,B,C,D) that each consist of five replicates.
I have a few miRNAs, that turned
updated 2.4 years ago • Sarah
B2) and two mutants(Ein40 & Ein9) for Shade treatment.
Here is my code for the above:
library(edgeR)
library(reshape)
counts <- read.delim("sam2countsResults.tsv",row.names=NULL)
head(counts)
counts<-counts[counts
updated 11.8 years ago • upendra kumar devisetty
3. upload the data into R, create a `DGEList` object with the counts and run a DE analysis using `edgeR`
After creating the `DGEList` I get an object like this one:
```
An object of class "DGEList"
$counts
L4_Input_1 L4_Input_2 L4_Input_3
updated 2.7 years ago • Assa Yeroslaviz
Hi,
I am working with multi-factor RNA-Seq experiment in `EdgeR` to find diff. expressed genes. The samples were processed in different batches (see below). I am trying to compare two different
updated 21 months ago • Abdul
Hi everyone,
I have data from metagenomic experiments: pyrosequencing of the 16S gene (454 GS Junior Roche). This gene was sequenced for 44 samples divided in 2 treatment groups A and B. The number of patients studied is 22, and for each patient one sample received the treatment A and another sample received the treatment B. So, we have paired data.
The reads from 71 bacterial species…
updated 9.3 years ago • eleonoregravier
Hi,
I am analyzing RNA-Seq dataset using `EdgeR` package and have a question about filtering by `filterByExpr` that would keep important genes based on a variable column
updated 18 months ago • mohammedtoufiq91
Good evening BioConductor ListServ,
I am interested in using edgeR to generate a single list of genes differentially expressed between treatment and control and either of two time...Good evening BioConductor ListServ,
I am interested in using edgeR to generate a single list of genes differentially expressed between treatment and control and either of two time points...help me understand these d…
updated 9.7 years ago • Matt McNeill
__Little background__
I have used edgeR quite some time now and try to teach others to use it as well. Most of them are familiar with hypothesis testing, means...__Little background__
I have used edgeR quite some time now and try to teach others to use it as well. Most of them are familiar with hypothesis testing, means, variances
updated 6.3 years ago • Mr.RB
Hi! I conducted DGE analysis between 2 groups of cell lines MYCN amplified vs MYCN non amplified.
Cell lines in the MYCN non amplified group had these FPKM values for MYCN gene: 5.182582, 3.104376, 4.962478
Cell lines in the MYCN amplified group had these FPKM values for the MYCN gene: 101.2204, 301.8182 , 280.6712
Now visually there is a marked difference between these two groups and s…
recently been trying to normalizing large metagenome abundance matrices with the function cpm(y) of edgeR. I get the following error:
<code>Error in .isAllZero(counts) :<br/>
long vectors not supported yet: memory.c:3438<br/>
Calls
div class="preformatted">
Dear all,
I have a problem using edgeR with the following experimental design:
I have 14 isolated cell types from 14 different donors.
I am interested in expression
I am trying to do a classic test for significant differential gene expression in edgeR 3.34.0, as implemented as a bioconda package that I am invoking in a versioned environment. I have two different versions...quite* work, because of that one "robust=TRUE" in an otherwise functional batch file:
```
# Load edgeR:
library(edgeR)
# Import data:
setwd("/ocean/projects/mcb190015p/schwarze/Ace…
updated 3.1 years ago • Erich
Hello!
we are using the exactTest in edgeR with TMM normalization to compute differential expression for smallRNA-Seq data. We have 3 experimental conditions...what we characterize as novel miRNAs.
We performed differential expression analysis separately in edgeR for the 373 known miRNAs, the 1132 (373+759) known and novel micro RNAs and the 94,300 loci which contains everything...dra…
updated 9.0 years ago • Sam
of the genes differentially expressed (3 control vs 3 treatment). I used the TMM normalization and EdgeR for the analysis, which assume a maximum of 60% of differentially expressed genes. How to proceed with such a case? Should
updated 7.5 years ago • aec
hi,
the documentation of the aveLogCPM() function from edgeR says that this function is similar to:
<pre>
log2(rowMeans(cpm(y, ...)))</pre>
because CPM values may be more disperse than logCPM
updated 7.0 years ago • Robert Castelo
div class="preformatted">Hi,
I am trying to figure out how to do comparisons using edgeR but have
to admit that I am on unsure ice.
My experiment is abiotic stress on two genotypes (E and J) and these
have been sampled
updated 10.1 years ago • Guest User
Hi,
I am currently attempting to perform a differential expression (DE) analysis using edgeR for phip-seq data. The analysis involves comparing multiple samples with bead-only samples.
some of the samples lack
updated 18 months ago • f_rahmdani
have done this right? Is
age.L the fold change in gene expression with increasing age?
> library(edgeR)
> library(limma)
> targets<-read.delim (file="coding_targets.txt")
> targets$age<-factor(ordered (targets$age))
>
updated 12.8 years ago • Shona Wood
repeat type A. I have read the following threads
[Modeling input data in ChIP-seq experiments with EdgeR, DESeq(2) or Limma][2] and [Question: DESeq2 for ChIP-seq differential peaks][3] and it seems like the general consensus is that
updated 4.4 years ago • mkmwong
Hello, I am running a glm analysis with edgeR on 64 biologically independent samples, with 3 factors. I have sex (M and F), age (P0, P7, P15, P30), and genotype (Control, Knock...Hello, I am running a glm analysis with edgeR on 64 biologically independent samples, with 3 factors. I have sex (M and F), age (P0, P7, P15, P30), and genotype (Control, Knock-Out
updated 3.9 years ago • jackiesalzbank
I am using the edgeR for 2 datasets, but one dataset is a subset of another one. I have 3 different diet (D1, D2, D3), and 3 time points (T1, T2, T3).
One dataset
updated 2.8 years ago • bioinformaticssrm2011
Good morning,
I am analyzing RNAseq data from 2 different populations exposed to 2 experimental treatments. I get the following error when running edgeR: "error in dispCoxReid(y, design=design, offset=offset, subset=subset, : no data rows with required number of counts." After this error is reported, R freezes and I must force quit the program. Im not using this function in my code so I am unsur…
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