The tximport vignette describes the following steps for using the data with edgeR:
https://github.com/mikelove/tximport/blob/master/vignettes/tximport.md
<pre>
library(edgeR)
<span style="line-height:1.6...counts</span>
normMat <- txi$length
normMat <- normMat/exp(rowMeans(log(normMat)))
library(edgeR)
o <- log(calcNormFactors(cts/normMat)) + log(colSum…
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for the platform and as usual, I may have your few minutes to my question?
I used both DESeq2 and edgeR to analyze my RNAseq data. However, I found a higher number of significant genes in my DESeq2 analysis compared to edgeR...and please show me my mistake case I missed something.
My variable(sample) is continuous data.
```
## edgeR
x <- DGEList(counts = muscle, group = Sample)
…
This error has been discused a number of times on this list. The
solution
>> is to upgrade edgeR to the current devel version.
>>
>> Also please see the Bioconductor posting guide:
>>
>> http://www.bioconductor.org...at="" gmail.com="">
>>> To: bioconductor at r-project.org
>>> Sub…
smallRNA library deep sequencing data and trying to identify
differentially expressed miRNAs, using edgeR package. I have 24
different
samples with 2 biological replicates (48 libraries). I am performing
multiple group comparison...once I
set
my DGE list or I could proceed without any normalization? I assume in
this
case that edgeR performs a default normallization when it is
"calculating
lib…
updated 12.0 years ago • Danie
span style="line-height:1.6">I am trying to reproduce the results of DiffBind for edgeR analysis.</span>
A member of my research group did analysis with DiffBind and got nice results, whereas me, performing...edgeR separately could not get any results.
DiffBind was called as follows:
<pre>
WNN_vs_WEN= dba.analyze(WNN_vs_WEN)
</pre>
According...to DiffBind protocol: …
of these
sequences
(create a 'base-level abundance'), and then input the new abundances
into edgeR to identify sRNA sequences that have been enriched in the
samples (i.e. have been transferred rather than contamination...Analysis design:
The workflow is basically following:
http://cgrlucb.wikispaces.com/edgeR
+spring2013
1. Get the total counts of sample specific sRNA sequences in all
samples
an…
updated 11.1 years ago • Kenlee Nakasugi
nbsp;
Hi,
I did my analysis using EdgeR and with DESeq2 with and without lfcShrink. At FDR<10% we have the following:
EdgeR - 17 genes
DESeq2 without LFC shrink...LFC shrink - 54
Only 10 genes overlap between all the 3 methods at FDR<10%. The fold change for EdgeR and DESeq2 without LFC shrink are almost the same for these 10 genes are high. But when the analysis is r…
updated 6.0 years ago • Akula, Nirmala NIH/NIMH [C]
Hi all,
Aaron - thank you for the excellent csaw package and extensive users guide! I am analyzing a ChIPSeq experiment that has 60 IP samples + 60 inputs. There are 3 treatments X 4 brain regions = 12 groups X 5 reps each. It seems a shame not to use the input samples and I was following section 3.5.3 to compare the scaled average of the IPs to the scaled average of the inputs. However, I'm wor…
updated 6.2 years ago • Jenny Drnevich
div class="preformatted">Hello,
I'm using edgeR for analyzing RNA-seq data containing Control (CR) and
two
Treatments (HR and SR) with 2 replicates for each.
Based on the...with DE
analysis?.
Here is the code I used and my sessionInfo().
Thank you !
Avinash
library(edgeR)
x <- read.delim(filetxt, row.names=1, stringsAsFactors=FALSE)
group = factor(c("CR", "CR", "HR", "HR", "SR", "S…
too big.
This could arise, for example, if your counts are less dispersed than
Poisson, because edgeR can't estimate dispersions to be less than
zero.
This of course would suggest a problem with the source of your data.
With...more usual data, it is very hard to imagine how correct use of
edgeR
could lead to a gof plot like you attach.
Best wishes
Gordon
On Tue, 9 Oct 2012, Thomas Frederick W…
I'm currently working with data coming from deep sequencing of 48
small
RNAs libraries and using edgeR to identify DE miRNAs.
I could not figure out how to design my matrix for the following
experimental design:
I have 2 varieties...and
both
varieties in the 3 different locations.
I was wondering if I could use the section 3.3 of edgeR user guide as
reference or if someone could suggest me any …
updated 11.9 years ago • Danie
Hi,
My question is whether the statistical methods used by edgeR are suitable for detecting significant differences in abundance of UNIref protein family features as generated...have a continuous metadata variable which I would like to correlate with gene family abundance using edgeR/Limma-Voom. I can't see why this wouldn't be a suitable method, but would welcome outside input on this.
HUM…
Hi,
Does anyone have experience with standard rna-seq analysis tools (edgeR, DESeq2, etc) to detect allele-specific expression? I have a count table in which each F1 hybrid (3 biological replicates...counts for the paternal and maternal allele. I am considering implementing a paired design in edgeR to test for differential allele expression between the parental alleles. However, I have…
I am using edgeR for analyzing shRNA data. So far I got the DE pvalue per shRNA. Now I want to summarize the results per gene rather than...I am using edgeR for analyzing shRNA data. So far I got the DE pvalue per shRNA. Now I want to summarize the results per gene rather than per...I am using edgeR for analyzing shRNA data. So far I got the DE pvalue per shRNA. Now I want to summarize the result…
updated 9.6 years ago • vladot
Hi,
I'd like to use together EDASeq,RUVSeq and edgeR
I'd like to know if It's correct to run the folling code
According to EDASeq manual:
<pre>
dataOffset <- withinLaneNormalization...need the result from EDASeq but I still want to Remove Unwanted Variation
so I __modify __the edgeR paragraph of the EDASeq manual:
<pre>
W_1 <- pData(set1)$ W_1
pData(…
I am using edgeR to look for differential expression. I am struggling to export data generated in edgeR (specifically DGELRT-class...I am using edgeR to look for differential expression. I am struggling to export data generated in edgeR (specifically DGELRT-class information, produced after the QL F-test) and convert it to .csv file.
The edgeR package has excellent documentat…
updated 8.5 years ago • cellbiologyhelp
<div class="preformatted">Hello Gentlepeople,
I have been using the edgeR package to identify differentially
abundant
tags in an RNA-seq experiment.
I was happy when the edgeR package version 2.4.6 called 41
differentially
abundant tags.
However, now I am unhappy because the same analysis with edgeR package
version 3.0.2 does not call any differentially abundant tags.
I've compared the …
div class="preformatted">Dear all,
I use edgeR for differential analysis of ChIP-seq densities.
I would like to know how to export the results from 'exactTest',
including
Hi
I am using edgeR in an R package and as per suggested by the R programming conventions I have edgeR as a dependent package in my DESCRIPTION...the package.
I noticed that at least one function (in this case cpm()) performs differently for the edgeR::cpm() and the explicity imported library(edgeR) followed by cpm(). For example,.....
---
> counts <- matrix(runif(100…
Hello,
I am new to the field and wonder what the differences are between edgeR and limma as both are recommended for RNA-seq and other applications.
Tried reading the papers and manuals but my stats...is limma so much faster, does this has to do with the models`?
- Does limma estimate a dispersion as edgeR does? Because this seems to be the part that in edgeR takes very long when you have many g…
updated 2.5 years ago • jose.carmeliet
div class="preformatted">Dear Peter (or Shan Gao),
Short answer:
You are using an old version of edgeR. You need to either install the
current version of edgeR from Bioconductor or, with the version you
have,
you can use
write.table...result$table, etc)
instead of write.table(result, etc).
Longer answer:
This is not an edgeR bug. The topTags results object has been
produced
correct…
where we need already batch corrected expression values e.g. network analysis?
1. CPM
library(edgeR)
dge <- DGEList(counts=count)
dge <- calcNormFactors(dge, method = “TMM”)
logCPM <- cpm(dge,log=TRUE,prior.count
updated 7.1 years ago • ashwini.kumar
<div class="preformatted">Dear list,
I am analyzing RNA-Seq data with edgeR for a typical two factors
design:
$samples
group lib.size norm.factors
R4.Hot HotAdaptedHot 17409289 0.9881635
R5.Hot HotAdaptedHot 17642552 1.0818144
R9.Hot ColdAdaptedHot 20010974 0.8621807
R10.Hot ColdAdaptedHot 14064143 0.8932791
R4.Cold HotAdaptedCold 11968317 1.…
<div class="preformatted">
Hello R and edgeR users/developers,
I had a question regarding the use of edgeR and graphing results. I'm
trying to do some comparisons between including and excluding
different features in edgeR. One variation I'm trying is the
following:
x <- read.delim("fileofcounts.txt",row.names="Symbol")
group <- factor(c(1,1,2,2...div class="preformatted"&g…
updated 10.6 years ago • Guest User
div class="preformatted">Dear Professor de Pillis,
The SAGE data is bundled with edgeR, but not by these names. See:
https://stat.ethz.ch/pipermail/bioc-sig-
sequencing/2011-August/002180.html
The data also...2009.
Best wishes
Gordon
------- original message ------------
Tue Jun 3 20:48:26 CEST 2014
Dear edgeR people,
I've just installed edgeR 3.6.2 following the instructions from
http…
<div class="preformatted">Hi All,
I am pretty new to edgeR, this is the first time I use the package,
as
well as the first time I try to find differential expression using
RNA-Seq
data...div class="preformatted">Hi All,
I am pretty new to edgeR, this is the first time I use the package,
as
well as the first time I try to find differential expression using
RNA-Seq
_bias corrected counts without an offset_” from the tximport vignette to use my tximport counts in edgeR: Would i still need to execute the edgeR `` calcNormfacotrs() `` method?
As far as I understand it would not be necessary, because...files, type = "salmon", tx2gene = tx2gene, countsFromAbundance = "lengthScaledTPM" )
dge <- edgeR::DGEList(counts = txi$counts, group = grouping_…
After normalizing the data with TMM method in edger one gets lots of values <1. Unfortunately, I found neither in edger manual nor in edger paper the description how the
updated 8.7 years ago • tonja.r
<span style="line-height:1.6">Hi,</span>
I was wondering how to use edgeR to perform equivalence tests. I would like to compare two groups and extract genes that are significantly similar. I...span style="line-height:1.6">Hi,</span>
I was wondering how to use edgeR to perform equivalence tests. I would like to compare two groups and extract genes that are significantly simi…
updated 9.5 years ago • roberto.spreafico
about 20%.
>I did the batch tests pairwise exactly as if they were different
genotypes.
>
>edgeR reported about 4x as many differentially expressed genes as
>sage.test. But there was almost no overlap with any...gt; and the same genes were up/down regulated (on the whole).
>> >
>> > Then I ran edgeR on all 4 samples. A large …
but for others I do not. I've created
a
design matrix as described on p32 of the 27 October 2012 edgeR user's
guide, but when I try to estimate the common dispersion using
estimateGLMCommonDisp() it tells me:
"Error in glmFit.default...gt; comparisons both within and between patients. I have included a new
> section in the edgeR User's Guide based on your experiment that
> describ…
Dear all,
Upon comparing my results for the analysis between DESeq2 and EdgeR, I have realized that the 2 results obtained after DEG analysis are extremely different from each other. The thresholds...of all the genes reported to be upregulated in both packages; 30% are common between the 2 packages (EdgeR and DESeq2)
2. Conversely, when comparing genes reported to be upregulated in DESeq2 and r…
and then copy them to be the NormFactors for the p and r samples. Is
copying them like this telling edgeR to re-compute the library sizes?
It
doesn't seem to be happening because the lib.size before and after
these
commands
Hi,
I noticed that both edgeR and limma have function to perform differential splicing analysis based on exon level counts. I am wondering why exon...are used instead of splice junction counts (i.e. STAR SJ output). Would it be ok to perform an edgeR or limma analysis using splice junction counts?
Thank you
I am currently using the edgeR package for RNASeq analysis, however, I have a bit of a problem. In the current dataset that I am working on, I noticed...dispersion. Any feedback on as to why this may be occurring is greatly appreciated. I am using edgeR version 3.22.5. Many thanks, Lisa.
<table>
<tbody>
<tr>
<td> </td>
</tr>…
I am currently researching the differences in RNA-Seq data analysis,
comparing the two well known EdgeR and Voom methods. However, there is
one
thing I can not manage to reproduce, namely the logCPM value in the
output
of the...LRT table of EdgeR, after analyzing a certain contrast or
coefficient. I understand from the manual and helpfile, that this
logCPM
value
expression for each of the 2 files.
i used both programs to analyse differential expression.(edgeR &
DESeq)
i have a problem in the results..(maybe you can help me..)
i used this manual http://manuals.bioinformatics.ucr.edu...lt;= 0.05, ]
sigDESeq <- na.omit(sigDESeq)
sigDESeq <- as.character(sigDESeq[,1])
library("edgeR");
group <- factor(c(1,2))
cdsR <- DG…
Hi All,
I analyzed my data RNAseq data with edgeR but I like the ease of visualization by cummeRbund.
I was wondering if there is a way to transform "fit output" and  ...Hi All,
I analyzed my data RNAseq data with edgeR but I like the ease of visualization by cummeRbund.
I was wondering if there is a way to transform "fit output" and the...normalized coun…
updated 7.5 years ago • alakatos
div class="preformatted">Dear edgeR people, I've just installed edgeR 3.6.2 following the
instructions from
http://www.bioconductor.org/packages/release...GSM755.txt, GSM756.txt
yields no results. These files do not seem to have come bundled with
the
edgeR package. Could you please point me to where I can find these
files?
I am running R 3.0.2 (2013-09-25) on Mac OSX.
Thank you!
L.G
When I try install EdgeR along with DESeq2 and limma I get the following errors and I cannot find suitable threads online to help me solve the...code 1 (use -v to see invocation)
make: *** [edgeR.so] Error 1
ERROR: compilation failed for package ‘edgeR’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/edgeR’
ERROR: dependency ‘genefilter...package ‘genefilter’ had …
if I may ask a question that may have been asked before, it is about basics of limma and edgeR :
sometimes in the documentation and in some examples, the design matrix is specified as :
1) design <- model.matrix(~group
onto my spike-in control expression. What is the best way to do this?</span>
d.RNA <- edgeR::DGEList(counts = round(counts), group=group)
d.Spike <- edgeR::DGEList(counts = s)
 
updated 9.2 years ago • R
I tried using the processAmplicons function from edgeR where the hairpin sequence is at start in the fastq file and the barcode towards the end. While there are 100% matches...I tried using the processAmplicons function from edgeR where the hairpin sequence is at start in the fastq file and the barcode towards the end. While there are 100% matches with...with why the hairpin sequences aren't bein…
updated 2.2 years ago • Claire.Prince
div class="preformatted">Dear all,
I'm doing an EdgeR analysis and made some GOF plots after estimating
geneewise dispersion and fiting my data. I noticed that my values
I am just trying to learn more rna-seq statistics and R, so I am playing around with the data in edgeR. I have paired samples. When I do plotMDS, few of the paired samples appears very close to each other i.e ( indvidual\_1\_treated...of drug is not shown any difference in that individual ? How to interpret this ?
<pre>
library(edgeR)
raw_counts <- read.table("raw_count_matrix…
Hello,
In DEG analysis using edgeR or limma, is there a requirement on the minimum number of samples to compare?
Can I just compare 1 treatment against 1...Hello,
In DEG analysis using edgeR or limma, is there a requirement on the minimum number of samples to compare?
Can I just compare 1 treatment against 1 control
updated 5.7 years ago • jzhan067
2. mapping mutant vs wild type genome
3. obtain gene counts
4. compare gene counts using edgeR or deseq tools
Maybe other tools are more suitable
updated 8.3 years ago • biotech
now Iam trying to analyse my MeDip data set using Diffbind and Iam quite confused whather to use edgeR or DESeq2 for the analysis (iam a biologist with zero training in statistics and bioinformatics try to teach himself...if I get ride of false postive or i simply loss positiv peaks. Is there a rule of thumbe when to use edgeR or DESeq2.
Thanks for any suggestion
I am trying to run edgeR with the GLM on some data that I've already used with the 'classic' edgeR analysis, as I would like to try it with RUVSeq. ...However, I am getting the following errors when I attempt to use the edgeR estimateGLMCommonDisp function:
Error in mglmLevenberg(y, design = design, dispersion = dispersion, offset = offset, ...think it's a data issue. I…
a RNA-seq analysis so tried to install differents pkgs. Unfortunately I'm not able to install "edgeR", I've looking for any possible solution but i hasn't success, I would be really thankful for any kind of help.
Thank you!!
these...BiocManager", quietly = TRUE))
+ install.packages("BiocManager")
> BiocManager::install("edgeR")
'getOption("repos")' replaces Bioconductor standard repos…
updated 2.5 years ago • alam
files, each of two different time points I am trying to
look at. How do I input these data into the edgeR program so that I
can see the matrix? I hope this question makes sense.
Audra
-- output of sessionInfo():
> sessionInfo
function
Dear edgeR users,
I am not an experienced R user. I ran the edgeR for the TCGA RNAseq data using raw count from the Rsubread...Dear edgeR users,
I am not an experienced R user. I ran the edgeR for the TCGA RNAseq data using raw count from the Rsubread featureCounts and the TCGA miRNAseq data using raw count from TCGA level3 data to iden…
Hello, Dears,
I may ask a quick question on the edger?
1. Does edger support continues variables as DESeq 2 does?
2. Do you think the number of differential expression genes...from edger different from DESeq 2?
I just want to compare my result got from DESeq 2 with adger?
Thanks,
Amare
updated 4.5 years ago • Do it!
div class="preformatted">Hi,
I am using edgeR for DGE analysis and I have two samples with two
replication.
I was successful in passing through the following codes
div class="preformatted">Dear All,
First, wish you all a very happy and prosporous New Year.
In EdgeR manual[Case Studies section], for two group comparison,
generally
exactTest usage is shown, whereas for the multiple
<div class="preformatted">Thank you for your answer! Moving forward I removed the lane that I
verified by plotMDS to be different from the other two. I have 2
further
questions.
1) I have a few highly expressed genes - the 2 most highly expressing
genes
make up 23 and 10 percent of all mappable reads, respectively. Do I
need to
do something to make sure that these genes will not have a neg…
lt;- crash_objs$norm_factors
print(sessionInfo())
# This will generate a segmentation fault.
edgeR::cpm(count_mat, norm_factors * colSums(count_mat))
```
Output:
```txt
Loading required package: limma
trying URL 'https://bimsbstatic.mdc...memory not mapped'
Traceback:
1: cpm.default(count_mat, norm_factors * colSums(count_mat))
2: edgeR::cpm(count_mat, norm_factors * colSums(count_mat))
An …
preformatted">I just wanted to check if RNA Seq counts generated using RSEM, are a
valid
input for edgeR package?
--
Maria Dermit
Ph.D. Student, Luscombe group
EMBL-European Bioinformatics Institute
Wellcome Trust Genome
remaining non-outlier genes. To use it,
you
will need to switch to the quasi-likelihood routines of edgeR. You
will
also need to update to the Bioconductor 2.12 versions of edgeR and
limma
rather than the older Bioconductor...that the quasi-likelihood approach is (deliberately) somewhat
more
conservative than the classic edgeR exact test, but it should still
have
plenty of power to get good res…
<div class="preformatted">Dear Prof Smyth,
in
design <- model.matrix(~ a + b + a:b , data=targets)
my interest is in factor a (coef=2).
""Do you expect the effect of experimental factor b to be same for
each level of a? If yes, then maybe you don't need the interaction
term. It depends on your experiment and on the questions you want to
ask.""""
I am not sure, but I guess the…
Recent ...
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Answer: Gene expression analysis of parents offsprings with multiple tissue types
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James W. MacDonald
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This support site is primarily intended to help people with technical software issues rather than analysis of specific datasets. You could …
Comment: Error in GOmeth function of missMethyl when EPICv2 annotation is used
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thanks, will give it a try
Answer: Harmonizing RNA-seq data of different sourceS(cell vs. tissue) to further conduc
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James W. MacDonald
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Your question is off-topic for this site. You might try over on biostars.org instead.
Answer: Student
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deeenes
▴
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An alternative is to use [`OmnipathR::translate_ids`][1] (developed by me):
```
library(OmnipathR)
library(magrittr)
metabolites <- data.…
Comment: Inconsistent result in edgeR
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hiroko.ohmiya
•
0
Thank you so much!
I understand the result after calculating CPMs.
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