library
has detected my use of a dynamically loaded .so, and has reverted to
serial
behavior? Or is edgeR preventing it's functions from being fork'ed
somehow?
Thanks in advance,
-Aaron
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Order by: Relevance
div class="preformatted">I am experimenting with edgeR for high throughput (next gen) sequence
data and proteomics spectral count data and have a few questions.
1. Is it correct...the pseudocounts (pseudo.alt produced by
estimateCommonDisp) as normalized counts? According to the edgeR
vignette ?The pseudocounts are calculated using a quantile-to-quantile
method for the negative binomial so …
updated 15.7 years ago • Ann Hess
morning all,
I am just starting to analyse my first set of RNA-seq results and am
trying to use EdgeR to do this. I have spent time reading the vignette
and manual and working through it using our data. The design of our
experiment...the contrasts we expect (i.e. there is no "Ap" or "France") and I
think that this might be because EdgeR is using the first level of the
factors of Genotype and Lea…
Hi,
I performed differential transcript expression analysis using `edgeR` pipeline. I usually use workflow from the `edgeR` workflow; [4.6 Differential transcript expression of human lung adenocarcinoma...Hi,
I performed differential transcript expression analysis using `edgeR` pipeline. I usually use workflow from the `edgeR` workflow; [4.6 Differential transcript expression of human…
updated 5 months ago • mohammedtoufiq91
y$counts-floor(y$counts))
[1] 0
I have also posted the session information as below. Both the R and
edgeR package are the most recent versions. However, the results are
still the same as before.
Are there other possible reasons...max(y$counts-floor(y$counts))
It also isn't clear that you have installed the current version of
edgeR.
Have you installed R 3.1.0? Can you please give the sessionIn…
that are not sufficiently expressed
y <- edgeR::DGEList(counts=Y)
y <- edgeR::calcNormFactors(y)
edgeIt <- function(group)
{
nr.states <- length(unique(group))
group <- as.factor...f <- stats::formula("~group")
design <- stats::model.matrix(f)
y <- edgeR::estimateDisp(y, …
updated 7.3 years ago • Ludwig Geistlinger
<div class="preformatted">Dear Bioconductor Authors,
I fitted a generalized linear models using glmFit() in edgeR. I wanted
to extract the estimated fisher information matrix (or the estimated
inverse fisher information matrix) from the fitting. The function
approx. expected.info() in edgeR seems to be the right function to
use. However, I have two problems when using it: (1) It does not w…
understand the choices when using qunatification pseduoaligners like Kallisto for per-gene estimates. EdgeR official documentation mentions that we can use Tximport "which produces gene-level estimated counts and an associated...edgeR offset matrix". In another place I read that EdgeR ignores estimated normalization factors if it detects provided offsets
updated 5.1 years ago • ognjen011
Hi everyone,
I am trying to install edgeR on my M1 Mac, however I got this error:
```r
Loading required package: limma
Error: package or namespace load failed for ‘edgeR...unable to load shared object '/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/edgeR/libs/edgeR.so':
dlopen(/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/edgeR/libs/edgeR.so, …
updated 3.0 years ago • Onur
<div class="preformatted">Dear Daniel,
The guidelines are the same for miRNA-seq as for RNA-seq. At its
simplest, you simply need a reasonable minimum number of counts in at
least some samples. At a minimum, I think you would want at least 5
counts, maybe more, in each sample in which the gene in expressed.
So, if your sequencing depth is about 20 million reads per sample, you
might ask…
updated 11.5 years ago • Gordon Smyth
<div class="preformatted">Dear Edger developers and users,
I would like to compare transcription levels of orthologous genes
belonging
to different species, in order to find significant species-dependent
changes in transcription levels. I though of using Edger for such
analysis.
Specifically, I have the read-counts data for several RNA-Seq samples,
for
2 different species (e.g., read...di…
updated 11.3 years ago • assaf www
<div class="preformatted">Dear edgeR Users,
I have RNS-Seq count data by genes, 4 treatment groups (each with 2
biological replicates) and two factors (E: C or H, and...div class="preformatted">Dear edgeR Users,
I have RNS-Seq count data by genes, 4 treatment groups (each with 2
biological replicates) and two factors (E: C or H...A: 13 or 25).
And I
applied the GLM model of edgeR with …
updated 12.8 years ago • Ari Eszter
<div class="preformatted">
Hi,
I have been working with edgeR to find differentially expressed genes
for RNA-seq data. I have been working with a data set with 3 treatment
groups and...div class="preformatted">
Hi,
I have been working with edgeR to find differentially expressed genes
for RNA-seq data. I have been working with a data set with 3 treatment
groups...The samples were
sequen…
Thanks for preparing the guideline on edgeR. However, I did not see any information supporting continuous variables in edgeR. May I know does edgeR supporting below
updated 5.1 years ago • Ivy
div class="preformatted">
How suitable is edgeR for analyzing RNA sequencing data obtained from
multiple studies, possibly using multiple platforms?
I am trying...RSEM-processed
data for cancer-specific sub-projects (each with 200+ samples).
I am trying to use edgeR for differential expression analyses with
Exact test, using 'raw count' values in the two cancer data-sets as
the input...for e…
updated 12.8 years ago • Guest User
working on RNA-seq data.
I am trying to go through a differential gene expression analysis
using EdgeR and starting with 2 conditions * 2 replicates = 4 runs
(illumina, mapped with bowtie on known reference genome). I have few...exactTest() run the differential analysis (performing negative
binomial test). But according to the edgeR manual, those two functions
called the equalizeLibSizes() functi…
updated 13.4 years ago • François RICHARD
div class="preformatted">Hi,
I would be grateful for some input on using edgeR for small RNA
sequence data. I have been testing edgeR on a set of miRNA data (3
groups with n=10, 15 and 15). After removing genes
div class="preformatted">Hi there,
I'm an amateur edgeR user, and I'm having trouble generating a heat
map for
the differentially expressed genes. All examples that I've looked
<div class="preformatted">Hello,
I have used edgeR for DGE analysis and also generated plotSmear. I
guess by
dufault the plotSmear shows red dots for differentially expressed...div class="preformatted">Hello,
I have used edgeR for DGE analysis and also generated plotSmear. I
guess by
dufault the plotSmear shows red dots for differentially
Hi there,
Would anyone know the correct way to create a citation for [edgeR user manual][1] ? I wasn't sure whether to cite the original edgeR paper or if the user manual needs a separate citation?
Thanks...1]: https://www.bioconductor.org/packages/devel/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf
updated 20 months ago • k___
I am so new in using R and edgeR. I calculated the logFC in edgeR using the following code:
```
targets <- read.delim("cell_line_M.txt", stringsAsFactors...the strategy suggested in [here][1] like:
FC=sqrt(8*7)/ sqrt(7*4) --> logFC=log2(FC) = 0.49
but edgeR suggest logFC=0.2
Can anyone guide me if in a wrong way I am or i missed anythong?
[1]: https://www.biostars.org/p/342756
div class="preformatted">
Hi,
I have been trying to create a DGEList object in edgeR, using the
following command:
> tar<-read.delim("test_target.txt")
> b<-readDGE(tar)
Error in readDGE(tar) : Repeated...tags are unique using awk '{print$1}' |
sort|uniq and yet I keep getting this error.
I have used edgeR successfully in the past and am currently also able
to us…
div class="preformatted">Hi All,
I am using edgeR for the DE analysis and in the user guide I noticed
to use
the following code:
sum(p.adjust(de.common$table$p.value, method
<div class="preformatted">
Gordon K Smyth <smyth ...="" at=""> writes:
>
> Hi Mahnaz,
>
> Why don't you follow the advice of the edgeR User's Guide (as Mark
has
> suggested)? All the case studies in the User's Guide describe how
the
> filtering was done in a principled way.
>
> Total count filtering is not so bad, but it is sus…
Hi Naomi,
Thanks for your interesting questions about the edgeR model.
1) We assume that variability in RNA-seq counts come from three
sources:
a) sampling variability associated with...Hi Naomi,
Thanks for your interesting questions about the edgeR model.
1) We assume that variability in RNA-seq counts come from three
sources:
a) sampling variability associated with sequencing (for each …
updated 3.5 years ago • Gordon Smyth
Running R ver. 3.4.0, after generating an error message with an edgeR load, I updated bioconductor and then re-installed, i.e. via biocLite("edgeR")
library(edgeR) produced the following error...Error: package or namespace load failed for ‘edgeR’ in get(Info\[i, 1\], envir = env):
lazy-load database '/Users/adamfreedman/Library/R/3.4/library/edgeR/R/edgeR.rdb' is corrupt...In get(In…
updated 8.5 years ago • afreedman405
I was reading blog posts, manuals and tutorials to find a good DEG pipeline.
I thought edgeR was a good choice and tximport was good to summarise my transcript level abundances,
but then I saw this tweet from a...I was reading blog posts, manuals and tutorials to find a good DEG pipeline.
I thought edgeR was a good choice and tximport was good to summarise my transcript level abundances,
bu…
all 36 possible
combinations. I have count data for all cell lines. So whether I
should
analyze by edgeR or DeGseq? Can I perform exact test/GLM on this sort
of
data.
I am very new to analyze this kind of data and I would appreciate
Dear all,
I am a edgeR user and I would like to know if edgeR reports 'average' cpm for each of the conditions tested in the analysis. Having a look
updated 8.7 years ago • Anna Esteve Codina
<div class="preformatted">Sorry to resurrect a somehow old thread, but I wanted to kick the
tires on this and wanted to clarify the google-record for posterity
... so:
On Sun, Jul 20, 2014 at 5:18 PM, Gordon K Smyth <smyth at="" wehi.edu.au="">
wrote:
>
> On Mon, 21 Jul 2014, Gordon K Smyth wrote:
>
>> logCPMc <- removeBatchEffect(y, batch)
…
updated 11.4 years ago • Steve Lianoglou
div class="preformatted">Hi,
We are examining the use of edgeR to analyze allele-specific count
data from RNASeq experiments. In these studies, each biological
replicate (n=18) has...bias.
My question relates to how to best handle the normalization of the
counts in this case. EdgeR applies calcNormFactors to the columns,
which disrupts the maternal:paternal count ratio for each gene in eac…
updated 11.6 years ago • Christopher T Gregg
with me. Regarding differential gene expression analysis from RNA-seq experiment, as far as I read, edgeR accept raw count and normalize with TMM method, is it right? However, I read in a paper used edgeR for differential expression...one of samples stands out from the rest, please let me know if we normal these data before running edgeR analysis?
Thank you in advance
&…
updated 9.8 years ago • Sara
div class="preformatted">
I am new to R and edgeR. I am trying to follow to example
9. Case Study: deep-sequenced short tags from the edgeR manual.
I download the data from
last year. Do we still need to set the prior
when looking at comparatively large data sets? Or is edgeR less
smoothing in the latest version.
thanks
Simon.
>
>
> On Wed, 9 May 2012, Gordon K Smyth wrote:
>
>> Hi Simon,
>>...gt; least 2 cpm in >= 10 samples, that may take care of the one-offs.
>>
>> Second…
div class="preformatted">Hi Gordon,
I was looking in the devel code for edgeR and I noticed this new check
in glmQLFTest:
> if(!is.null(disptype)) if(disptype=="tagwise") stop("glmfit should
be
computed...same dispersions and such, due
to
this quote from the glmQLFTest help text in the current release of
edgeR:
> [glmQLFTest] behaves the same as ?glmLRT? except that it repla…
Dear Mete,
No, you cannot use non-integer counts with edgeR.
If you must use non-integer counts, please use the voom() function in the limma package instead. This will do an analysis...that is not too different from edgeR, just a little less powerful, and is not bothered by non-integer values.
Best wishes
Gordon
__Edit__: more recent versions...of edgeR do now allow non-integer counts. How…
updated 7.1 years ago • Gordon Smyth
count matrix which element is the number of reads within
gene region for each data set.
I applied edgeR and DESeq methods for this comparison.
For this case,
1. edgeR uses Poisson by setting common.disp=1e-6 (zero).
2. DESeq still...NB by assuming there is no difference b/w two
samples to estimate dispersion.
The results are
1. edgeR identifies many genes with very small p-values / adjusted
p-…
div class="preformatted">
Dear list,
I am using EdgeR to calculate differentially expressed genes of RNAseq
data.
the toptags output gives me both a p-value and an FDR value
I have several questions about tximport results used for edgeR.
According to the tximport vignette, the ideal method is to provide the estimated counts from the default condition...with an offset that corrects for changes to the average transcript length across samples for edgeR analysis. Your example of creating a DGEList for use with edgeR is as follows:
<pre>
library(edgeR)
cts &…
you mean by single nucleotide based normalization,
however the following comments may be helpful.
edgeR automatically adjusts for library sizes, whether you include an
explicit normalization step or not. Normalization...is a separate
issue,
and is intended to deal with more subtle issues.
Normalization, as edgeR does it, does not require replicates.
Best wishes
Gordon
> Date: Fri, 04 …
updated 14.9 years ago • Gordon Smyth
step.
I would like use the total read count normalization method to
normalize the data then use the edgeR to test my multi-factor models
as in my previous post. The total read count normalization is given as
X_ij/(N_j/mean(N))=X_ij...gt; To: bioconductor at r-project.org, mlinyzh at gmail.com
> Subject: [BioC] EdgeR multi-factor testing questions
>
>
> Dear Gordon,
&…
updated 11.9 years ago • Guest User
div class="preformatted">Dear Bioconductors,
I'm trying to use edgeR to compute the differential expression from
some
RNA-Seq data, but it seems to be generating some odd results.
I'm running...edgeR on data on about 6000 genes, across 5 experimental
conditions. When I compute the differential expression for any two...of
these
conditions edgeR it is returning a 'nan' fold-change for about 15…
updated 14.2 years ago • Nick Schurch
of TF. TFs were mapped using the CUT&RUN method.
To do the differential analysis we used EdgeR and TMM normalization. However, in one case where there is more total level of TF in one condition compared to the other...to incorporate spike-in normalization. Does anyone know how to incorporate spike-in normalization to EdgeR differential analysis?
Thank you
updated 5.1 years ago • Hesh
Due to the increase in functionality in edgeR, I've become slightly confused about the correct order of calling the different functions, since there seems to be multiple...also has an argument called `` robust ``, which is suggested to be set to `` TRUE `` in the edgeR user guide. Is running `` estimateDisp(robust=TRUE) `` similar to running `` estimateGLMRobustDisp ``? </span>
To…
updated 9.8 years ago • maltethodberg
div class="preformatted">Dear the edgeR community,
Good day.
1. Could someone please light me, does the "topTags" show also the
down-regulated genes/tags in the top
div class="preformatted">Hi,
We are working on a glm analysis in EdgeR and voom() and I am hoping
we can help with our design. Currently, we are getting errors.
We have 18 RNA-Seq biological replicates...and father B,
and nine samples have mother B and father A.
we wish to test the following models in edgeR and voom()
(~sample+allele+parent) vs (~sample+allele)
(~sample+allele+allele:pare…
div class="preformatted">Dear edgeR community,
Good day.
Please forgive me if I ask a stupid question.
May I ask, using trended dispersion to estimate genewise
i was trying to using trinity to do Differential Expression Analysis, which need to install the edgeR first.
After installing the package with two steps:
> source("http://bioconductor.org/biocLite.R")
 ...gt; biocLite('edgeR')
i got some error messages as following:
BioC\_mirror: http://bioconductor.or…
Dear Iddo,
No, it is not valid to use a different design matrix for the
dispersion
estimation.
edgeR will handle your model with 400 samples, but it will admitedly
be
slow. If this is too slow, then switch to voom() in the limma...package,
which will be very fast, or to glmQLFTest() in the edgeR package,
which
will still be relatively slow but faster than the glm routines in
edgeR
(or DESeq2).
…
limmaWorkflow.html#normalising-gene-expression-distributions)[ easy as 1-2-3 with limma, Glimma and edgeR" ](https://www.bioconductor.org/packages/release/workflows/vignettes/RNAseq123/inst/doc/limmaWorkflow.html#normalising...to assess if using spike-ins for normalization would be informative I performed normalization with edgeR and limma-voom (quantile or spike-ins), boxplots:
[![N…
updated 7.0 years ago • Konstantinos Yeles
at="" wehi.edu.au="">
>From: Jenny Drnevich <drnevich at="" illinois.edu="">
>Subject: edgeR with only 1 replicate?
>
>Hi Mark and others,
>
>Can edgeR be used if you only have 1 replicate per group? If not, do
>you
updated 16.4 years ago • Jenny Drnevich
<div class="preformatted">
Dear all,
I am currently trying to use easyRNASeq in order to create a DGElist
object for edgeR. However, when I run the function on my samples (as
shown below), I encounter an error message AFTER counting:
Preparing output...Dear all,
I am currently trying to use easyRNASeq in order to create a DGElist
object for edgeR. However, when I run the function on my s…
updated 13.1 years ago • Guest User
div class="preformatted">Hello list,
I'm trying to use read counts normalized with edgeR outside R. After a
DGEList has been normalized by TMM and dispersion has been estimate
(at least with estimateCommonDisp
about either using normalized counts from EDASeq or raw counts with offset values of EDASeq in edgeR GLM for differential expression. I read edgeR manual where it says:</span>
"The correction factors may take the form of scaling...sizes. Alternatively, gene-specific correction factors can be entered into the glm functions of edgeR as offsets."
Also it is mentioned that estimateCo…
div class="preformatted">Hi All,
I am working on sRNA-seq data and with no replicates and using edgeR
to
identify differentially expressed tags and using an arbitrary BCV
value
(0.3) based on suggestion in edgeR manual...replicates. "
But I came across this post which mentions a conservative way to
calculate BCV:
[BioC] EdgeR: general advice on using edgeR for sRNA analysis:
https://stat.eth…
div class="preformatted">
All,
I am a new edgeR user. I have difficulty understanding the meaning of
the ???cpm??? function of edgeR package. I mean I understand that
each
but has been troubling me for a while. How is fitting a negative binomial glm in R different from edgeR DE analysis. I think edgeR allows one to model a different variance for all genes, which is not feasible in the standard...glm.nb I can analyze all the samples together using drug and disease as two factors (0/1). However, edgeR only allows pairwise comparisons, such as between cases with no dr…
I'm unable to load edgeR even if it installs correctly. I'm new to this field so a lot of things might be naive. thank you in advance for any help!
```
Error...package or namespace load failed for ‘edgeR’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Library/Frameworks/R.framework/Versions/4.2-arm64...Resources/library/edgeR/libs/edgeR.so':
dlopen(/Library/Frameworks…
updated 3.1 years ago • Vittorio
at="" dundee.ac.uk="">
> To: bioconductor at r-project.org
> Subject: [BioC] Problems with edgeR for differential expression.
>
> Dear Bioconductors,
>
> I'm trying to use edgeR to compute the differential expression...nature produce
> '-inf' or 'inf' fold-changes, not 'nan' fold-hanges, and 2) in some
> cases edgeR is calculating a 'nan'…
updated 14.2 years ago • Gordon Smyth
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