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
Order by: Relevance
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
updated 12.3 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
updated 8.1 years ago • Jenny Drnevich
<div class="preformatted">Dear Ben,
glmLRT() allows you to specify the contrast to be tested in two ways.
If
the contrast happens to correspond to a column of your design matrix,
then
it is one the original coefficients and you can just specify which one
using the coef= argument. Otherwise you can use the contrast=
argument to
specify any contrast, using a numerical vector of the same len…
updated 12.9 years ago • Gordon Smyth
Hi there,
I'm using edgeR version 3.10.2 to analyze my RNAseq data. I have a design in which there are two factors (habitat and watershed) with two...interaction between them, I am using a design matrix (shown below) modelled on section 3.3.4 of the edgeR users guide:
(Intercept) habStream shedRobe…
Hi: I'm trying to identify differentially methylated CpGs between two different treatments. I've been following the edgeR vignette as well as the Chen et al. 2018 paper but am running into confusing results depending on how I code the model matrix...to identify differentially methylated CpGs between two different treatments. I've been following the edgeR vignette as well as the Chen et al. 2018 p…
updated 5.2 years ago • sabrina.mcnew
Hello!
I have followed the example reported in edgeR guideline, section "4.1 RNA-Seq of oral carcinomas vs matched normal tissue". I have 54 pairs of tumor and normal matched
updated 6.8 years ago • Pingu
that your question was specifically about the DESeq package,
but
you have previously asked about the edgeR, bayseq and DESeq packages
on
SEQanswers:
http://seqanswers.com/forums/showthread.php?t=4349
so I thought you might...a more complete answer.
I think that edgeR is the only package on Bioconductor that analyses
RNA-Seq experiments with multiple explanatory factors.
In your...you asked …
I was using edgeR for an exact test (output to a variable "et"), done by exactTest() function. Then I used goana(et, species='Hs') function
only a few dozen differentially expressed genes when I
analyze my RNA-Seq data with DESeq2 (79) and EdgeR (34) (even fewer
when
I use EBSeq). I had expected many more -- hundreds or even a thousand.
If this is the real answer, I'm fine with...are the ranges of numbers of
differentially
expressed genes that one would expect from DESeq2 or EdgeR?
More information:
I'm in the midst of my first RNA…
of each microbe in the above data sets.
I was wondering if I could take the count data and use edgeR to calculate the foldchange of the organism?
Say, I may get staphylococcus aureus is 3 log2FC upregulated in treatment
updated 4.3 years ago • megha.hs28
define replicate
Group = paste(S,Time,Time.rep,sep="_")
#$#$ define group_time_replicate
library(edgeR)
#$#$ load edgeR package
f.factor = data.frame(files = names(f.dat), S = S , Time = Time,
lib.size = c(apply(f.dat,2,sum)),norm.factors =
calcNormFactors...as.matrix(f.dat)))
#$#$ make data for edgeR method
count.d = new("DGEList", list(samples = f.factor, counts =
as.matrix(f.dat)))
#$#$ …
updated 12.1 years ago • Guest User
but also at any time in one test, following the section "3.3.3 Treatment effects over all times" of edgeR user guide.
The design of the experiment is 3 biological replicates for each of the 3 samples:
<table border="1" cellpadding...a whole comparison to find genes responding to the treatment any time in a single test.
I am using edgeR.
This is the code I am using:
targets <- is th…
of two factors, time (4x time points) and genotype (7x genotypes), that I am analyzing with edgeR. Each time point/genotype was sequenced with 3x biological replicates (84 samples total).
<pre>
# meta data for design
meta...lib.size <- colSums(e$counts)
e$samples</pre>
Following section 3.3.1 of the users guide for edgeR, I combined all the experimental factors into one co…
updated 9.4 years ago • rghan
td>
<td>34</td>
<td>NA</td>
</tr>
</tbody>
</table>
I would prefer to use DESeq2 (or EdgeR) for this, based on good prior experience with this software
Of course for each SNP, multiple individuals are homozygous
Dear all,
I am analyzing RNAseq data, using the edgeR package 3.26.8 (in R 3.6.1).
In total I have several hundred samples (cell lines) to which I assigns labels, based on some...Dear all,
I am analyzing RNAseq data, using the edgeR package 3.26.8 (in R 3.6.1).
In total I have several hundred samples (cell lines) to which I assigns labels, based on some secondary
updated 5.0 years ago • d.ricken
I have a question about the meaning of interaction terms in design matrix on the page 38 in the edgeR User's Guide. In line 19, the guide say: "The last two coefficients give the DrugvsPlacebo.1h and DrugvsPlacebo.2h contrasts
updated 5.2 years ago • 2002ymx02
div class="preformatted">Hi EdgeR community:
I'm reading the edgeR
manual<http: bioc="" doc="" edg="" edgerusersguide.pdf="" er="" inst="" packages="" release="" vignettes="" www.bioconductor.org
Hello,
I am new to the field and have a question regarding analysis of RNA-
seq data with the edgeR package. I am looking at the difference in
gene expression between two groups of patients (control and disease)
after...the highest
variation after stimuli between the two groups.
Based on the section 3.5 of the edgeR users guide, I first came up
with the following nested paired analysis:
--------…
into my automatized workflow.
For convenience reasons (automatic analyses), I do not specify my edgeR model with an intercept as recommended in the documentation.
Instead, I took inspiration from this sentence in chapter...G1 only, then temp1 VS temp2 in G2 only), is this acceptable ?
However, if I understood correctly edgeR's documentation, it is recommended to block G for direct comparis…
updated 6.2 years ago • rfenouil
div class="preformatted">Dear list,
I got the biological coefficient of variation (BCV) with edgeR by
calcualting sqrt(tagwisedisp).
I'd would like to compare it with the BCV given by DeSeq. However I am
not
sure what variable...is that I should obtain with DeSeq very similar
BCV
values for each gene to those obtained with edgeR, right?
Many thanks!
Miguel Gallach
[[alternative HTML…
a proband. I am interested in Proband vs
Control kind on analysis. I am using the latest release of edgeR.
=====================================================
Samples structure as follow:
Family 1 (COMPLETE)
Father, Mother, Sibling (Male), Proband
Family 2 (COMPLETE)
Father, Mother
and then compare that with the other genotype group.
Here is my code so far:
library(edgeR)
rawcounts <- read.csv("file:///input.csv", row.names = "gene")
group <- c(1,1,1,1,2,2,2,2)
y <- DGEList(counts = rawcounts, norm.factors
updated 8.6 years ago • ugwu.nelson
Hi,
I am treating NovaSeq-produced RNA-Seq data with edgeR. In the analysis I look at what I call “strain” effect. There are DEGs for this factor that I find are biologically hard to
updated 5.4 years ago • David Rengel
Hi, There:
We have RNAseq data with 4 cell lines with different knockout genotypes (WT, A, G, GA), and for each cell lines, we have two treatment types: treated (H) and untreated (C) with 5 replicates for each condition. we are interested in the treatment effect on each of these cell lines: WT.H_C, A.H_C, G.H_C, or GA.H_C (H_C mean treatment vs untreat). These are easily to be done in edgeR (s…
updated 2.2 years ago • Mike
zebra finch RNA-Seq data, using STAR for alignment, Rsubread-featureCounts for quantification, and edgeR for differentially expressed analysis. However, I don’t know how to run edgeR to read an R List object produced by featureCounts
updated 6.4 years ago • Gary
Hello,
I have RNA-seq experimental data with the following variables (and the number of each in parentheses):
1. Treatment (3)
2. Distance from base (9 per repetition)
3. Repetition (4 per treatment)
To be clear, for each of the three treatments, there were 4 repetitions (individual trees) each, and from each of those repetitions, leaf tissue was collected from the tree at varying…
updated 3.4 years ago • erik.burchard
My experimental design consists of four groups and two experimental factors (+/+, +/-, -/+ and -/-). In addition, each group has four biological replicates (the first biological replicate of each group was taken at the same time, the second replicates at another and so on) and a clear batch effect between replicates.
My design matrix looks like this:
design <- model.matrix(~batch+factor.…
updated 9.8 years ago • Ekarl2
design <- model.matrix(~batch+A\*B)
My headers include "ALoA" and "BLoB"
From reading the EdgeR User Guide (particularly the Arabidopsis case study, pp. 61-68), I suspect that this would indicate that HiA is set as the
updated 9.4 years ago • Ekarl2
<div class="preformatted">Hi Ryan,
edgeR can't.
voom can, but you have to put it together partly yourself. Just fit
voom
to each timepoint separately, then cbind the voom output objects back
together.
Or else just proceed in edgeR as if the dispersions are equal across
timepoints. This will be conservative but won't give false positive
results.
Best...<div class="preformatted">H…
div class="preformatted">Hello everyone,
I'm trying to compare limma vs edgeR in finding tissue specific genes
from my RNAseq samples. For edgeR I've followed directions from a
previous post and...have managed to get good results. The thread is
named
"edgeR: finding tissue specific genes" and here is the link:
http://permalink.gmane.org/gmane.science.biology.informatics.conductor...18
element…
Hi,
I have a TMM (trimmed mean of M values) CSV file of whole RNA sequencing (generated by edgeR package) with two groups (group A with 27 samples and group B with 18 samples). Each samples is in one column and each gene
updated 3.1 years ago • hamidrezarazzaghian
plot trends between genes across different conditions from my normalized count matrix (featurecount-EdgeR).
I was using "csCluster" in cummerbund. Now I switched to this pipeline and I am wondering, if similar pacakage or tool is
updated 6.1 years ago • thindmarsmission
nonallergic.Medium,
levels=design)</pre>
When I read about the design formula and matrix in edgeR, I understood that the blocking should be set up like this:
<pre>
design <- model.matrix(~0+ patient + group)</pre>
Unfortunately
updated 6.0 years ago • anou
Dear Bioconductors,
I am working on the differential gene expression among Drosophila species after parasitization with wasps. I am following the EdgeR tutorial, and recently updated the package to edgeR\_3.8.6 (R version 3.2.2) where some changes were introduced for the estimation of dispersion and quasi-likelihood test. I am interested in both: 1) the (orthologous) genes tha…
updated 8.9 years ago • lauraalazar
is not a transformation. It is specific
to
the log-linear modelling approach used in edgeR. It does not
transform
the count data into a form that can be input to permutation-based
statistical methods designed...for pathway analysis of microarray data.
The edgeR User's Guide says
"These adjustments are offsets in the models used for testing
DE and do not transform the counts in...other
…
updated 12.5 years ago • Paolo Guarnieri
glm I would write it like this: ~condition/sample/technical) but I am not sure how to do it in edgeR
I tried
design<-model.matrix(~condition + technical, data=target)
fit <-glmFit(d,design)
lrt<-glmLRT...this is correct because my technical replicates should be nested within sample.
From the edgeR userguide, I got th…
updated 9.6 years ago • silvia.paolucci81
<div class="preformatted">I am analyzing paired samples (RNA-seq). I am facing problem with
edgeR at
y <- estimateGLMTrendedDisp(d, design) step where it is saying error
message "Error in t(y) + prior.count.scaled : non-conformable...div class="preformatted">I am analyzing paired samples (RNA-seq). I am facing problem with
edgeR at
y <- estimateGLMTrendedDisp(d, design) ste…
data, and have a question about setting thresholds using filtering by expression on genes in `edgeR`. I like this function, and by default, I set the below for my experiment set-up:
keep <- filterByExpr(y, group=Treatment_Timepoint
updated 17 months ago • mohammedtoufiq91
From: Natasha Sahgal
Sent: 11 September 2012 18:26
To: 'bioconductor at r-project.org'
Subject: edgeR multifactorial design: confusing BCV plot
Dear List,
This is a follow up from my previous post:
https://stat.ethz.ch/pipermail
sin) - atan(groupB:cos/groupB:sin),
levels = design
)
```
within the framework of edgeR? Alternatively, is it somehow possible in the modeling step to specify a model like
```model.matrix(~ group + group * sin(t + phase
updated 4.9 years ago • ingerslev
Hello, I am analyzing an experiment and am trying to come up with a model design to compare the differences between 2 treatments and 2 factors. I need help in trying to organize the model design matrix in EdgeR. How can I write the code for them to be recognized? I also need to make sure my replicates are similar to one another in each...between 2 treatments and 2 factors. I need help in trying t…
updated 5.9 years ago • cody0071
different time point.
```r
expr = DGEList(counts, group)
logCPM <- cpm(expr, log = TRUE, prior.count = 3)
fit <- lmFit(logCPM, design)
fit.eb <- eBayes(fit, trend = TRUE)
fit2 = contrasts.fit(fit, my.contrasts)
fit.eb = eBayes
___Please help me in that.
==============================================
library(edgeR)
Read\_counts=read.delim("Table.txt",row.names = "Gene")
counts=subset(Read\_counts,Read\_counts$Control >= 10 | Read\_counts
updated 8.9 years ago • Sushant Pawar
<div class="preformatted">how to design a model matrix and test by edgeR
dear all:
my data is composed of 35 samples, have two factor
time and treatment
1. The first question is
i want to find DE genes...div class="preformatted">how to design a model matrix and test by edgeR
dear all:
my data is composed of 35 samples, have two factor
time and treatment
1. The first question is
i want …
updated 12.3 years ago • wang peter
<div class="preformatted">Dea Gordon, Ryan and Nicolas,
Than you all for the detailed advice.
I have one more question regarding the blocking factor model. In my
case I
have, actually, 2 external factors to consider - one is the platform,
the
other one are the subjects.
My sample matrix is the following (I've attached the CSV in case you
can't
view the image):
I am only interested in co…
updated 10.2 years ago • Nick N
21, 2014 8:59 AM, "Sander [guest]" <guest at="" bioconductor.org=""> wrote:
> >
> > Dear edgeR maintainers,
> >
> > I have some troubles setting up the correct design for my DE
experiment.
> I now how my experiment...should have both positive and
negative
> values, not just zeros and ones.
>
> See the edgeR …
as I usually do for differentially expressed gene analysis), using the results of cpm() function in edgeR package? If so, how? After the gene filtering and TMM normalization, should I use voom() in limma package to transform log
updated 6.8 years ago • Frocha
Hi everyone I am have RNA seq data that I am trying to analyze using EdgeR. Here is the codes I used to analyze the data I just want to make sure that the codes are right and that I can rely on the output...lt;- read.csv("celldata.csv", check.names=FALSE, sep=",", header=T, stringsAsFactors=FALSE)
library(edgeR)
library(limma)
rownames( counts ) <- raw.data[ , 1 ]
> y <- …
updated 8.6 years ago • MEM
**The setup:** ChIP-seq for histone marks in two closely-related cell lines which represent certain developmental stages.
**The problem:** We know from cytogenetics that one of the cell lines has genetic anomalies such as triplicated chromosome1 (trisomy) that will/would (probably) increase the counts originating from peaks at that chromosome by roughly 33%. Input samples (so total chromatin i…
Dear experts!
I am performing an EdgeR analysis in TCGA samples. I have a subset of the 83 patients I want to check their differential expression in comparison...This is the code I used during my analysis.</span>
<pre>
library(TCGAbiolinks)
library(edgeR)</pre>
<pre>
query = GDCquery(project = "TCGA-COAD", data.category = "Transcriptome Profiling",
…
Hello,
I'm using edgeR (in the Trinity-RNA Seq Pipeline) to do a differential expression analysis and when I try to make a heatmap I got the following
updated 7.8 years ago • cvergarapulgar
SM, WS, WB) and I'm finding some unexpected results when comparing the three tests provided by the edgeR package: exact test, glmLRT, glmQLF.
Usually, as a preliminary exploratory analysis, I perform all the three tests mentioned
updated 9 months ago • Marianna
We have TagSeq libraries of a fungus with 5 replicates in two conditions: the fungus “in vitro” growing in plant extract and “in vivo” when it’s infecting its host plant. We actually have three fungal strains (race 2, race 3 and race 4), but at this point we’re mostly interested in what genes are “up-regulated” or “down-regulated” in vivo. In vitro libraries range in size from 3,034,612 - 5,796,…
updated 5.7 years ago • lepstein
<div class="preformatted">Dear Vincenzo,
Unfortunately I don't think I can answer that. Perhaps others on the
List could help.
BW,
Natasha
From: Vincenzo Capece [mailto:vivo0304@gmail.com]
Sent: 01 October 2012 09:04
To: Natasha Sahgal
Subject: Re: [BioC] DESeq - working with more than 2 conditions
Thanks a lot Natasha, edgeR is exactly what I was looking for.
I am also a statistics beg…
<div class="preformatted">Dear List
I have peak counts from RNA-IP samples and corresponding inputs, for
two
different conditions.
I would like to find DE-binding between the two IP conditions after
removing the differential expression effect.
In a previous post (titled "differential binding question") Mark
Robinson
suggested to do GLM analysis.
Before doing the DE analysis I have to normal…
Hi EdgeR developers and all,
I'm testing RNA-Seq data with the following factors:
treatmentA , with the categories 0,1
treatmentB
updated 8.1 years ago • assaf www
But because I don't have replicates I cannot use voom. Is it OK to use the log2(cpm) I obtained from EdgeR instead of those obtained by voom?
Thanks
updated 8.0 years ago • Camila Orellana
I am trying to use edgeR to analyze differential gene expression from my RNA-seq dataset and I get the following error, please help me out
```r
# >
updated 3.7 years ago • Rishav
Recent ...
Replies
Comment: Volcano plot has many values around zero
by
Michael Love
42k
It's positive over zero or nearly so.
Answer: Volcano plot has many values around zero
by
swbarnes2
★
1.4k
You've got genes with supposedly have a 32-fold difference, and the adjusted p-values are < 1x10-10? That seems odd.
Comment: Volcano plot has many values around zero
by
mjun
•
0
Why this cluster close to 0 with low p value is so distinctive. Is this common? What does it mean and why? Thanks
Comment: Volcano plot has many values around zero
by
swbarnes2
★
1.4k
I don't think this is evidence that the dataset is invalid. It's evidence that your experiment is underpowered, and/or your experimental c…
Comment: Differential Expression Analysis with unbalanced batches without replication bet
by
Gordon Smyth
51k
Have you read the totalVI documentation?, which says:
> **Important**
> We do not recommend using totalVI denoised values in other differ…
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