days.
Since I had too many differentially expressed genes, ¿Should I be more
conservative assigning edgeR dispersion value? Also, there are
considerable
more up-regulated genes in *exvivo* than in plate sample.
See logFC_vs_logCPM...776707
>ambiguous 47
>too_low_aQual 0
>not_aligned 263637
>alignment_not_unique 0
- edgeR code:
library(edgeR)
files <- di…
Order by: Relevance
at r-project.org wrote:
> 9. TMM and calcNormFactors: Normalization in baySeq to match
> edgeR and DESeq (Smith, Hilary A)
>
Hi Hilary,
The 'edgeR' function 'calcNormFactors' used to contain an option for
'quantile', but
updated 12.8 years ago • Thomas J Hardcastle
D, E-B, C-A, D-C, E-C, D-A, or E-A comparisons in an
ANOVA
test.
If anyone can suggest a method on edgeR to perform ANOVA tests, that
will
be perfect. If not, can someone suggest other possible packages that
could
help me do
So... The reason I'm posting this is because my graduate advisor wants me to fully understand how edgeR constructs heatmaps that have three comparative groups as opposed to two, and I agree. Now, I am not the most experienced...the same way no matter how many groups you have?
Another thing that I need to understand is how edgeR constructs the heatmap itself. I have looked at the edgeR manual …
updated 11 months ago • ulin.1
I am wondering whether there are best-practices to use edgeR on single-cell (10X) data that were quantified with the Alevin module from Salmon, given that we want to use the inferential...Therefore, are there best-practices to import the inferential replicates from Alevin into edgeR and can we "sum" this inferential replicate information per single cell to the pseudobulk level
Hi, I have some doubts on cpm function in edgeR package. Given this initial part of the code:
> library(edgeR)
> data_clean<- read.table("unito.txt", header = TRUE)
>
>
Dear Bioconductor community,
I'm trying to analyze a RNA-seq dataset with edgeR after importing the Kallisto counts with tximport and using the offset matrix.
But I'm not sure if I'm using the offset...offsets for a log-link GLM
normMat <- sweep(normMat, 2, eff.lib, "*")
normMat <- log(normMat)
```
#edgeR: create a DGElist
```r
myDGEList <- DGEList(counts= myCou…
updated 5 months ago • Marianna
Hi,
I am writing a post because I encountered an interesting question when using edgeR. I want to analyze RNA-seq data gained from samples of two groups: control and treatment (inhibitor of a kinase). I want to...change as a molecule with a very small expression level, but this molecule is important.
I know edgeR needs data to be normalized (TMM) first. However, if there is a fold change, this …
updated 21 months ago • Yongqing
am concerned that such fold-changes may be exaggerated. I am aware that voom calculates CPM using a prior.count of only 0.5, whereas the cpm() function uses a default prior.count of 2, leading to FC shrinkage.
Which approach would
updated 20 months ago • vm
table (~16,500 genes), i.e. rows with a total count sum of 12 or less
have been trimmed off. Using edgeR, I find 2569 genes (1224 up / 1345
down) to be differentially expressed at FDR better than 0.05.
Ive noticed that in this list...identifies 1569
genes (719 up / 850 down) at padj<0.05. Of these 1569, 1544 are also
called by edgeR, so, excellent agreement. Relaxing the cutoff to
padj&am…
updated 12.2 years ago • Michael Salbaum
nbsp;Factor-1 is pre vs post treatment. Factor-2 is cured vs not-cured. When performing edgeR I input factors as pre, post, pre, post, etc. And lib-types were cured, cured, not-cured, not-cured, etc. I imputed "genes...had read counts 200 - all samples pre and post in not-cured animals had read counts 200). EdgeR correctly identified my markers fo…
updated 8.4 years ago • tminning
the University of Lisbon and I am performing
several analysis of differential expression (using edgeR). Reading
edgeR manual I am not sure about the dispersion value that I should
use. I am comparing libraries of the same species
updated 11.2 years ago • Guest User
<div class="preformatted">
Hello,
I am using EdgeR to analyse RNAseq data.
I would like to know whether I should use several paired analyses or a
blocking analysis for this...div class="preformatted">
Hello,
I am using EdgeR to analyse RNAseq data.
I would like to know whether I should use several paired analyses or a
blocking analysis for
I have been playing with the `edgeR::filterByExpr()` function to find out how it works.
If I understand the documentation correctly the following code should...the result I obtained. For some reason the result for Gene_2 is returned as FALSE:
```r
library(edgeR)
library(magrittr)
(group <- factor(rep(c("Ctrl", "Treated"), each=3)))
# [1] Ctrl Ctrl Ctrl Treated Treated Tr…
updated 3.9 years ago • Axel
<div class="preformatted">Dear list,
In edgeR, it possible to get CPM values after batch effect correction
(and after TMM normalization)?
Thanks a lot!
[[alternative HTML...div class="preformatted">Dear list,
In edgeR, it possible to get CPM values after batch effect correction
(and after TMM normalization)?
Thanks a lot!
[[alternative
i would like to confirm that this
small
difference is statistically significant?
How o do this using edgeR??
Thank you very much in advance.
Asmaa
[[alternative HTML version deleted]]
</div
updated 12.1 years ago • Asma rabe
treated.
I would like to perform an ANOVA. Could you please exemplify using some example code in edgeR?
Thanks in advance.
YK
updated 8.6 years ago • myprogramming2016
div class="preformatted">Dear All,
I'm running edgeR 3.0.8 and notice that the results are considerably
different than those from older versions. I realized that it was
on a Illumina GA and wonder how to
account for both technical and biological replication using edgeR.
The dataset consist of 48 individual samples (time series with 4-6
biological replica per time point, 9 time points in
Hi all,
Please provide me the commands of ___"edgeR" ___for differential express analysis without Replicate
updated 8.8 years ago • Sushant Pawar
<div class="preformatted">Dear Adriann,
It isn't an artifact. You are simply seeing a few genes for which the
dispersion is estimated to be zero. EdgeR puts these dispersions to a
small positive value. They are not harmful.
You could also try
estimateDisp()
which will automatically estimate the prior df for you. This function
also has a robust option. If you turn it on, then it …
<div class="preformatted">
Hello everyone!
I'm just starting my MSc and I'm new to bioinformatics! I'm currently
stucked in a DE analysis of Arabidopsis thaliana sRNA seq comparing a
wild type (control group) vs several different mutants (geneA, geneB,
geneC, doubleGeneAC, tripleGenesXYZ) with two biological replicates
for each group (12 columns in the counts table); for what I've been
loo…
updated 10.8 years ago • Guest User
or by the species? I'm not sure if I can consider the samples
I grouped as "replicates" and
> use edgeR to do these tasks.
Just look at the plot and see where the samples fall. Do samples of
the same stage tend to group
together...gt; Zhe
>
>
>
> Dear Zhe,
>
> To do clustering of RNA-seq profiles using the edgeR packages, you
can use the plotMDS.…
updated 14.2 years ago • Gordon Smyth
<div class="preformatted">Hello List,
I'm trying to perform DE analysis using edgeR on the following samples
with
2 replicates per condition.
WC - Wildtype or Normal control
WI - Wildtype or Normal upon Infection...<div class="preformatted">Hello List,
I'm trying to perform DE analysis using edgeR on the following samples
with
2 replicates per condition.
WC - Wildtype or Normal co…
Dear Gordan,
I am writing to get your feedback on using normalized count as an input to edgeR algorithm. I understand that edgeR expects raw counts as input, and I wondered if there is a workaround in the pipeline
updated 4.2 years ago • sharvari gujja
am wondering if a ANOVA like analysis solve the purpose or if I should consider the glmQLFTest from EdgeR
updated 2.3 years ago • Mug_qd
div class="preformatted">Hello edgeR users,
I have been checking around to find out how to best analyze our data
as well as remedy our experiment design. It...our case because it does not have functions to handle time-series
data. It also relies very much on edgeR to do its job. So I think it
would be more flexible to use edgeR directly myself. Reading
edgeRUsersGuide.pdf, I found that...exam…
updated 10.1 years ago • Vang Le
Dear all,
I have performed edgeR differential analysis on RNA-Seq data with six samples (3 vs 3). edgeR finds around 30 up regulated genes but more than 100...and there's no such asymmetry in the number of down and up regulated genes. I have been told that edgeR assumes that the number of up regulated genes is similar to the number of down regulated genes - is that true?
Thanks!
Paul
I am trying to use a custom size factors (computed using the Scran package) in edgeR when doing the workflow for differential expression and get the following error:
d2=estimateDisp(d2,design.mat,mixed.df...it seems to work. I guess my real question is are these equivalent? My end goal is just to use edgeR differential expression on single cell data with the Scran normalization method
updated 8.2 years ago • mnaymik
<div class="preformatted">I've done standard rna-seq differential expression analysis on a gene
level
using edgeR. For downstream analysis I would like to extract the
normalized
counts for a particular exon. What is the best way to go...preformatted">I've done standard rna-seq differential expression analysis on a gene
level
using edgeR. For downstream analysis I would like to extract th…
Hi all, just a quick question on best practices to create datasets for
RNA-seq analysis with edgeR or limma:::voom().
I must create a table in which read counts for every entity (i.e.
every transcript) for every sample. In order
different from assuming Poisson variability.
You give a quote from the first case study of the edgeR User's Guide.
That data was from an observational study on human tumours, obviously
highly variable data.
Best wishes...Gordon
------------ original message --------------
[BioC] question about edgeR and Poisson model: common dispersion is
too low
Glazko, Galina V GVGlazko at uams.edu
Tue Apr 1…
nbsp;
Hello
Can anybody help me with following question
I am using Edger for DE analysis. In what situations will it not be possible to assess an DE-hypothesis with EdgeR?
kind regards
updated 7.4 years ago • johan.vanongeval
in `` normalizeChIPtoInput.R `` are missing `` list() `` at
https://github.com/Bioconductor-mirror/edgeR/blob/master/R/normalizeChIPtoInput.R\#L24
which will give an error
Error in return(p = rep(0, 1), scaling.factor = 0, prop.enriched
updated 7.6 years ago • dalerr
div class="preformatted">Dear EdgeR developers and kind list members,
I have a RNA-seq experiment which I would like to analyse using edgeR
as i think it is...a multi-factorial experiment .
After reading the excellent EdgeR user manual as well the wealth of
design-matrix related question in the mailing list, I am still unsure
about what design...was done on normal samples, hence
the unknown
…
Hi,
I have what I think are three simple questions regarding the goana() function of edgeR, which I am not very familiar with:
1-Does it work with Arabidopsis?
2- I understand that if the coefficient you are looking
Hi!
I'm doing some DE analysis via edgeR. There is one part I have some trouble to understand, and I suspect it may have to do with poor mathematical understanding...Or this is my goal anyway. In order to do this, I make use of the following function within edgeR:
decideTests(efit, adjust.method="BH")!=0
(0 in this case is genes that are not flagged as significant)
my understanding
updated 8.1 years ago • joseph.bergenstrahle
would you advise : could the normalization methods (TMM, etc) that are implemented in limma or edgeR (or DESeq2, or in other packages) be used for the normalization of 5C interaction data ? thanks,
-- bogdan
 
<div class="preformatted">Hi Mark and others ,
I am using edgeR to analyse one of my RNAseq data.
In this experiment, we have three tumour samples from three different
patients.
Named: Patient_1, Patient_2, Patient_3
We did RNASeq on Tumour-cells under two different conditions: treated
and
untreated, and wanted to find differential expressed genes after
treatment.
In the end, we got fo…
Hello,
I am interested in testing for differentially expressed genes with `edgeR` across multiple groups, using the ANOVA-like approach.
For example, in the mouse mammary gland experiment in the `edgeR...global"` and `"nestedF"`, which could be appropriate for this purpose; however, `decideTests` in `edgeR` does not have a similar argument.
One can use `glmQLFTest` repeatedly, selecting …
updated 4.3 years ago • jamie.gearing
div class="preformatted">I used edgeR to test differential expression of RNA seq data, but i
noticed some different between old version 2.2.5and new version2.4
all:
i have two questions
1. is the "size factor" from DESeq equally to the "norm factor" in the
edgeR
2. i can get the normalized counts by
counts(obj,normalized=T)
how to get normalized counts from edgeR
can i use the each
I have a data set of RNAseq performed on an Affymetrix HiSeq 2500, and am in the process of cleaning and pre-analysis, following the vignette from the edgeR package. The point where I'm stuck is in removing genes that are lowly expressed. There are 6 conditions in my data set; the...HiSeq 2500, and am in the process of cleaning and pre-analysis, following the vignette from the edgeR package. The …
updated 4.5 years ago • hcnbox
<div class="preformatted">
Dear Gordon,
before the last revision of the user's guide appears in the official
release of edgeR,
I just would like to make a correction : new page 31 it is 18 RNA
samples and not 9 RNA samples ( there are 9 patients, and 18 RNA...Dear Gordon,
before the last revision of the user's guide appears in the official
release of edgeR,
I just would like to make a corre…
some" without "tumor"
samples. I
want to remove batch specific differences between all samples. edgeR
however
gives me the same error, no matter how many samples I have in the
batch, but
does not give me this error if I remove...after
performing the linear regression on the batch factor? Can I then then
feed
the residuals into edgeR linear modeling? I want to compare how much
each
sample/patien…
updated 10.8 years ago • Eugene Bolotin
I just want to verify my code without replication using edgeR. Please check it and give your suggestions. it may help me to go forward.
*******************Thanks in advance***************************
library(edgeR)
rawpattihypo
updated 21 months ago • kuttibiotech2009
really sure if this design is correct. I've never seen
something like this. So I've also used the edgeR package using the
example 4.4 in the vignette.
library(edgeR)
Mouse<-factor(c("WT","WT","WT","WT","WT","WT","MT","MT","MT","MT","MT"
,"MT"))
Treatment...And I have 26 DE miRNAs
The problem here is that there is only 5 common miRNAs between DESeq
and edgeR.
Is the design correct ?wha…
Sample.Type`):
[Figure of PC1vsPC2][1]
So for differential expression analysis using edgeR, I thought it would be best to use `model.matrix(~Batch + Treatment)` for the model formula, where `Batch` represents `metadata...Exp.Date`, as per the [edgeR user guide][2] Section 3.4.3 *"Batch effects"*. However, unlike the examples in the edgeR user guide, I have the situation where...https://i.im…
updated 4.1 years ago • rebecca.lea.johnston
Hello,
I want to normalise my microbiome data (OTU table) using edgeR package and export my normalised matrix ( I want to test some normalisation methods, normalised data will serve to calculate...Hello,
I want to normalise my microbiome data (OTU table) using edgeR package and export my normalised matrix ( I want to test some normalisation methods, normalised data will serve to calculate bet…
updated 3.6 years ago • Pozdrawiam
div class="preformatted">Hi,
I am using EdgeR to find DE genes in an experiment with two factors
(Tissue (2 levels) and Treatment (3 levels). Currently the design
matrix...would like to specify a design matrix where a) I drop each of the
Treat
levels (in separate runs of EdgeR) to find the DE lists corresponding
to
each level of the Treatment and to b) specify a model where level1 of
the
Trea…
Is there a minimum number of gene identities required in
order
to analyze differential expression in edgeR?
Best,
Eleanor
[[alternative HTML version deleted]]
</div
updated 10.5 years ago • Eleanor Su
wondering whether I should manually adjust the BCV value to 0.5 or 0.6 for the exactTest function in edgeR.
Is it advisable to manually adjust the BCV value in this situation? If so, how should I choose the new value?
Also, to calculate...the BCV from the common.dispersion value in edgeR, the formula is simply `bcv = sqrt(edgeR_obj$common.dispersion)`?
Any advice would be appreciated.
…
updated 17 months ago • f_rahmdani
<div class="preformatted">Dear Laura,
Here is a reproducible example of edgeR code for finding genes that
are DE
between any of your cultivars, regardless of which cultivars:
nlibs <- 24
cultivar <-
factor(c(1,1,2,2,3,3,4,4,5,5,6,6,7,7,8,8,9,9,10,10,11,11,12,12))
design <- model.matrix(~cultivar)
y <- matrix(rnbinom(ngenes*nlibs,mu=50,size=10),ngenes,nlibs)
d &…
div>Hello ! </div>
<div> </div>
<div>I have used DESeq and EdgeR to get differentially expressed genes. </div>
<div> </div>
<div>For DESeq it is possible to put a design with more conditions...nbsp;+ cellType + MethodsUsed</strong></div>
<div> )</div>
<div> …
updated 7.8 years ago • bioinformatics
cases and controls.
-differences between treated and untreated.
5 tests in total. We can then use edgeR contrast function as something
like
this...
contrasts <- makeContrasts(
Case.TreatedvsUntreated = Case.Treated-Case.Untreated
div class="preformatted">It use to be that when you run deDGE from the edgeR library that it
calculated the Fisher exact p-values and put it in a slot "exact".
This
no longer seems to be the case, with
regarding using estimateGLMCommonDisp and
estimateGLMTrendedDisp.
It has been mentioned in the EdgeR manual[*Section 2.8.2 :- Estimating
Dispersion*] "Note that we need to estimate either common dispersion
or
trended dispersions
what is going on here. Do I need a more up to date version
of
limma for the development build of edgeR?
3)
>> Given your experimental layout with multiple groups but no
covariates,
you could use
>> the "classic" edgeR functions...be trusted and that something funny is
going
on. We are also getting strange results when comparing edgeR p-values
(from
either method) wit…
updated 13.0 years ago • Nick Schurch
div class="preformatted">Hi guys,
I would you to revise my edgeR code since it's possible I missed
something
important because being quite new on this.
Thanks, Bernardo
P.S. This questions...1067474
__ambiguous 0
__too_low_aQual 136484
__not_aligned 110488
__alignment_not_unique 0
############################################################
#edgeR
#######################################…
queries regarding design matrix for two group(Control vs.
KO)
Differential expression.I am using edgeR for this. Here is the ording
of my
question:- 1) Sample table for design matrix, 2) Design matrix, 3)
Questions.
*1) Sample table
Recent ...
Replies
Answer: Gene expression analysis of parents offsprings with multiple tissue types
by
James W. MacDonald
67k
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
by
s.malik
•
0
thanks, will give it a try
Answer: Harmonizing RNA-seq data of different sourceS(cell vs. tissue) to further conduc
by
James W. MacDonald
67k
Your question is off-topic for this site. You might try over on biostars.org instead.
Answer: Student
by
deeenes
▴
60
An alternative is to use [`OmnipathR::translate_ids`][1] (developed by me):
```
library(OmnipathR)
library(magrittr)
metabolites <- data.…
Comment: Inconsistent result in edgeR
by
hiroko.ohmiya
•
0
Thank you so much!
I understand the result after calculating CPMs.
Awards
• All
Popular Question to
micolak0115
•
0
Popular Question to
hayleyw
•
0
Scholar to
Lluís Revilla Sancho
▴
750
Popular Question to
Gordon Smyth
51k
Locations
• All
Italy, just now
Japan, 5 minutes ago
Australia, 6 minutes ago
Australia, 40 minutes ago
United States, 1 hour ago
Italy, just now
Japan, 5 minutes ago
Australia, 6 minutes ago
Australia, 40 minutes ago
United States, 1 hour ago
Traffic: 519 users visited in the last hour
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by the
version 2.3.6
version 2.3.6