div class="preformatted">
I recently used the EdgeR package to analyze a RNA-Seq dataset, with 2
genotypes and 3 biological replicates each.
After running the exacttest...value added to each gene for each sample or is
the added value different for different genes? How is prior.count
determined?
b) Are only genes that have a "0" in one sample moderated or all all
genes moderated by prior.count…
Order by: Relevance
Hello! I noticed in edgeR's NEWS that for the just-released edgeR 3.24.0:
<pre>
The default value for prior.count increased from 0.25 to 2 in...awhile to figure out why this was the case, because I was calling glmQLFit() and it does not have a prior.count argument, but following the ... led me to glmFit() where the default prior.count = 0.125. Changing the prior.count only...gt;…
updated 6.1 years ago • Jenny Drnevich
on the library size + 2 \* pseudocount (which was manually set to 0.5)
However, the cpm function in edgeR is slightly different when you want use
<span style="line-height:1.6">cpm(x, log=T, prior.count=0.5).</span>
It calculates the...following:
\# First scales the prior.count/pseudo-count and adds 2x the scaled prior count to the libsize
<span style="line-height:1.6">pri…
updated 10.2 years ago • John Brothers II
Dear all,
I'm using edgeR and I need to have a final cpm matrix with annotated IDs. Is there a way to not loose the iD information after doing
y<...Dear all,
I'm using edgeR and I need to have a final cpm matrix with annotated IDs. Is there a way to not loose the iD information after doing
y<-calcNormFactors...y) and logCPM<-cpm(y, log=TRUE, prior.count=2)?
I really need …
updated 7.4 years ago • abrantes.patricia
support.bioconductor.org/p/57416/
Dear Nick,
See ?exactTest and read the description of the prior.count argument.
For a little more detail, see ?predFC.
Note that division by zero is not undefined in R, it is just infinite...nbsp;(Inf). If you run exactTest() with prior.count=0, you will get exactly that.
Best wishes
Gordon
> Date: Fri, 31 J…
updated 10.0 years ago • Gordon Smyth
Hi everyone!
I'm trying to read the code of the functions being used in the EdgeR package during RNA-seq normalization and DE analysis. My background in statistics isn't very good and I like reading...this one is the following:
```r
aveLogCPM.default
function (y, lib.size = NULL, offset = NULL, prior.count = 2,
dispersion = NULL, weights = NULL, ...)
{
y <- as.matrix(y)
if …
updated 17 months ago • Josué
Hello Everyone,
I have a very noise RNAseq dataset with several covariates analyzed in edgeR.
<pre>
design <- model.matrix(~0 + conditions + cov1 + cov2, data=pheno)
d <- calcNormFactors(d, method ="TMM")
d <- estimateDisp(d...Hello Everyone,
I have a very noise RNAseq dataset with several covariates analyzed in edgeR.
<pre>
design <- model.matrix(~…
updated 6.9 years ago • alakatos
Hi,
this question relates to post [Time-course, comparison of two groups][1]. I have different question related to the data presented there so I've made new question.
I'd like to plot observed and fitted log-CPMs for a selected gene or genes.
I've consulted `edgeR` user guide (p. 113, the bottom block of code). But there is plot for one time series without replications.
I'd like to make a plot…
updated 21 months ago • boczniak767
Hi- Trying to run the `rpkmByGroup` function from edgeR, I get the error below.
rpkmByGroup(y, gene.length= rep(1000, nrow(y)))
Error in cpmByGroup.default(y = y, group = group, dispersion...group = NULL, gene.length, dispersion = 0.05, offset = NULL,
weights = NULL, log = FALSE, prior.count = 2, ...)
{
if (is.null(group)) {
group <- fact…
Dear all, I would appreciate any comments on the R code below that :
-- uses edgeR to measure the differential expression between siCTL and siPROTEIN
-- uses removeBatchEffect() function to correct...y <- y\[keep,,keep.lib.sizes=FALSE\]
y <- calcNormFactors(y)
logCPM <- cpm(y,log=TRUE,prior.count=3)
plotMDS(logCPM, col=as.numeric(subject))
logCPM <- removeBat…
pre>
require(edgeR) # edgeR_3.12.1
counts = "Sample1 Sample2 Sample3 Sample4
1 14 19 38 39
2 18 22 38 37
3 23 29 35 41
4 24 34 37 39
5 22 37 40 41"
design...3: glmFit.default(y$counts[sel, ], design, offset = offset[sel,
], dispersion = 0.05, prior.count = 0)
2: glmFit(y$counts[sel, ], design, offset = offset[sel, ], dispersion = 0.05,
prior.count = 0)
1: estimat…
updated 7.9 years ago • endrebak85
Hi,
I am working with RNAseq data using `EdgeR` (steps below), while I was discussing some preliminary data analysis and observations, I cam across a question about...gene length. Does EdgeR trimmed mean of M values (TMM) account for gene length along with the sequencing depth and RNA composition?
While I was...exploring more about this, I came across a couple of resources (links below):
…
updated 11 months ago • Sabiha
In the process of validating my procedure for using edgeR to calculate differential expression statistics; I've found that there are differences between the fold changes...In the process of validating my procedure for using edgeR to calculate differential expression statistics; I've found that there are differences between the fold changes estimated...calculated directly from the matrix of scaled…
nbsp;
Hello,
I have successfully run edgeR on an ATAC-seq dataset to identify differential open chromatin peaks across two cell types. I wanted to normalise for...the CQN package for normalisation steps. This creates a GLM offset to add to the DGEList object in edgeR that accounts for the normalisation.
The issue I have is that when I try to filter my DGEList object in edgeR to remove...I get …
vignette for tximport, and it has recommendations for how to import data for downstream analysis in edgeR, DESeq2 and limma-voom, but it does not mention the lesser-used limma-trend. The edgeR method stores the length corrections...or "lengthScaledTPM". The limmaUsersGuide() suggests doing `` logCPM <- cpm(y, log = TRUE, prior.count = 3) ``. I thought that since cpm() is an edgeR function …
updated 7.2 years ago • Jenny Drnevich
for calculating the context specific
average?
I really feel that you should not need to hack the edgeR code in this
way.
If the above hasn't already answered your questions, can you describe
more
precisely the plot you are...additional parameters and other default
values
>> than the ones you used:
>>
>> prior.count <- 2
>> dispersi…
Hi everybody, I'm using EdgeR to find differential expressed genes induced by diet.
I have two group (5 mice in standard diet (SD) and 5 mice in Diet1 (KD...respectively 2F+3M and 3F+2F
Analysis is carried out using the following code
```r
library(edgeR)
library(ggplot2)
#make DGElist
DG <- DGEList(matrix, group= group)
DG$samples$name= x$description
DG$samples$sex= x$Sex
…
updated 21 months ago • Giuseppe
Hello there,
I am working on DE analysis on two groups of total reads count from a RNAseq data using edgeR. I am not super experienced in edgeR, but I have used this same R script on some other dataset previously and that worked fine, but this time for some reason after I filtered out the non significantly differentially expressed genes (DE=0) in the edgeR output file, there are still 100+ gen…
I have seen many posts about batch effect correction on RNA-seq data. But I'm little confused in using the code for differential analysis. So, asking it here.
I have been using 8 rna-seq samples, 4 NOTCH silenced samples and 4 Controls. The setup is like this
Samples type days
1 Control day1
2 Control day1
3 Control day2
4 Control day2
…
updated 5.6 years ago • m93
Hi,
This question is about RNAseq analysis in `EdgeR` to identify common and specific differentially expressed genes. I have 3 different Donor's in-vitro cultured tissue...using RNAseq, then aligned and quantified. I now have a gene counts file ready to import into EdgeR RNAseq analysis pipeline. Using this data, I am interested in what are the common vs specific DEGs in response to virus...resp…
Overexpression EXP1
I have used following code for filtering and normallization:
library(edgeR)
group <- factor(paste0(coldata$Group))
y <- DGEList(counts,group = group)
## Filtering
keep <- rowSums(cpm(y) > 1) >= 2
table(keep...removeBatchEffect(y, design = design2)
## For Clustering Heatmap
logCPM &…
updated 5.6 years ago • Biologist
for differential expression analysis at the gene level.
The first approach (used with DESeq and edgeR) is to use the estimated counts from your quantification tool of choice, and let (or set) DESeq (or edgeR) use an offset to account...then suitable for use by voom (presumably these can also be used (but sub optimal) in the DESeq2 and edgeR world (right?)).
I'm curious about what version of the…
<div class="preformatted">Hi Gordon,
I used to use predFC() to get modified log count-per-million values
per sample but now I'm switching to cpm(). I just realized that
predFC() doesn't use the normalization factors in the DGEList object
when design=NULL, but it does appear to use them when the design is
specified (see example below) and there is no argument to specify
them, unlike cpm(). …
updated 11.3 years ago • Jenny Drnevich
div class="preformatted">Using edgeR can differentiate difference between Treatment and Control
using
a negative binomial assumption of the data. However...can edgeR be used
to
simulate data from the null?
--
Thanks,
Jim.
[[alternative HTML version deleted]]
</div
Dear Joanne,
If I understand you correctly, you want to filter features based on
cpm,
but you want edgeR to present to the results to you as if you hadn't
filtered. No, edgeR doesn't do that. So keeping track of which
windows
you...Best wishes
Gordon
On Wed, 28 Aug 2013, Joanne.Lee at csiro.au wrote:
> I'm using EdgeR to find differentially expressed reads within 100bp
> window…
<div class="preformatted">
Hi, all,
I remembered that I installed edgeR via bioconductor on June 2012 and
I used edgeR produce some data. Now I want to known which version of
edgeR that I once used. Does anybody know how to get this?
I am not familiar R, and I also tried the edgeR download page in
bioconductor. But I didn't get what I want.
Thanks and best wishes.
Guiling Sun
-- outpu…
div class="preformatted">
Hi there,
I have a question regarding edgeR - or it might actually be a more
general statistical question. In any case, I am using edgeR to analyse
my read counts and...It is, however, a little tedious
so my question here is whether this can be modeled and extracted in
edgeR's GLM ?
regards
JD
-- output of sessionInfo():
not relevant
--
Sent via the guest posting…
dim(x)
cpmCutoff <- round(1e7/mean(colSums(counts)), 2)
grpNum <- 2
x <- x[rowSums(edgeR::cpm(x) > cpmCutoff) >= grpNum, ]
dim(x)
x <- calcNormFactors(x)
range(x$samples$norm.factors)
logcpm <- edgeR::cpm(x, log = TRUE, prior.count...las = 2)
x <- calcNormFactors(x,method="TMM")
range(x$samples$norm.factors)
logcpm <- edgeR…
updated 16 months ago • nawaz.u.toyama
TMM") ``
`` v <- voom(y, design, plot=TRUE) ``
`` lcpm <- cpm(y, log=TRUE) ``
From EdgeR, it was recommended that lcpm could be used to generate heatmap with a prior.count. However, from https://f1000research.com
updated 6.2 years ago • Raymond
seq after limma for heatmap or cox or other downstream analysis, ***should I use the same way as in edger, jusr use the logCPM data here***
thanks a lot
dge <- DGEList(counts=mRNAdata)
dge <- calcNormFactors(dge)
**logCPM** <- cpm(dge...log=TRUE, prior.count=3)
v <- voom(dge,design,plot=TRUE, normalize="quantile")
fit <- l…
updated 4.3 years ago • linouhao
<div class="preformatted">
I am new to edgeR and I am not a statistician. I analyzed my RNA seq
data,
I got the results as 200 up regulated and 97 down regulated genes. My
questions are-
1. What is the cut off value used by edgeR to say upregulated versus
down
regulated? I am little bit confused here. When I checked the log fold
changes I couldn't...div class="preformatted">
I am new to …
div class="preformatted">Dear Bioconductor team,
I am using DESeq and edgeR for analysis of count data and find
differentially expressed genes and btw it worked very well. As input
data I created...the counts will be around 50x higher compared to the read
count
method.
By using the base counts in edgeR the number of differentially
expressed
genes is dramatically reduced. We normally compare D…
div class="preformatted">I could not run calcNormFactors in edgeR. Is this because I had a old
version of edgeR? I just installed the package last week.
Thanks.
Guoli Wang, PhD
CIT/DCB/HPCIO
I have RNA-Seq data which i mapped and used tophat for mapping splice
junctions,I would like to use EdgeR for identifying differentially
expressed genes.
Do you have an idea if i can use tophat out put file as input for
edgeR
Hello,
I have a question about the cpm function from edgeR. When I use this function with log = T, I get different results from when I use it without followed by log2 transformation...this? Why is that better than just adding 0.5 read count?
<pre>
> CPM <- cpm(DGE1, log = T, prior.count = 0.5, normalized.lib.sizes = F)
> tail(CPM)
DC07 …
preformatted">
1. If I enter source("http://bioconductor.org/biocLite.R")
biocLite("edgeR") in R package,
Does the R package automatically install the latest version, which
I
believe is 1.6.9?
2. While using readDGE...have very few read counts, I filter them out by
d<-d[rowSums(d$counts) > 1000,]
I wonder if edgeR compare tags which exist in one sample but are…
<div class="preformatted">Dear Li,
Your study doesn't seem to present any difficulties for edgeR, and the
analysis could be done as a whole.
If you would like more detailed advice, you would need to post the
targets
or samples...div class="preformatted">Dear Li,
Your study doesn't seem to present any difficulties for edgeR, and the
analysis could be done as a whole.
If you would like…
this code:
load(url("http://datos.langebio.cinvestav.mx/~cei/camera\_problem.rdata"))
library(edgeR)
camera(y, c(1,2))
__Error in qr.qty(QR, t(y)) : NA/NaN/Inf in foreign function call (arg 5)__
The full dataset actually has many lines...design0 <- t(qr.qty(QR, t(design))\[-1, , drop = FALSE\])
fit.null <- glmFit(y, design0, prior.count = 0)
zscoreNBinom(y$counts, mu = fit.n…
updated 9.8 years ago • Cei Abreu-Goodger
lab uses subread, which is better, faster and available as a
Bioconductor package.
You cannot use edgeR (or DESeq) to analyse base counts. The negative
binomial assumptions of those packages would be grossly violated.
However...at="" fli-leibniz.de="">
> To: bioconductor at r-project.org
> Subject: [BioC] BaseCounts & edgeR
>
> Dear Bioconductor team,
&…
div class="preformatted">Hi David
Yes, the logFC values given in edgeR are the log2 fold changes. To get
the non-log FC it is just 2^(logFC).
Best regards
Davis
--------------------------- Original Message
----------------------------
Subject: [BioC] edgeR...In the edgeR package fold changes rare given as logFC. Is that the
log2
value ? how can i get the non log FC ? is that 2^(logFC) ?
th…
I would like to carry out a GSEA analysis on some RNA-Seq data. I have
analysed the data using edgeR and have a list of regulated genes. The
data is paired - 6 biological samples, cells from each are infected or
uninfected...uses paired sample data I have followed the guidance for
this type of analysis in the marvellous edgeR manual. Searching for
advice on how to conduct GSEA I came across this …
Recipe for Differential Expression Analyses of RNA-seq Experiments Using Quasi-Likelihood Methods in edgeR"__ ([https://link.springer.com/protocol/10.1007%2F978-1-4939-3578-9\_19)](https://link.springer.com/protocol/10.1007...2F978-1-4939-3578-9_19)) and the filtering approaches implemented with edgeR.
So, in the specific part of the above pipeline, in section 3.4 :
___"Smalle…
updated 6.5 years ago • svlachavas
div class="preformatted">
Hi, I am new to the edgeR field and I do not know why it does not
work.
I have installed the R (latest version 2.15.0)and according to what is
mentioned...web site I use these two commands:
source("http://bioconductor.org/biocLite.R")
biocLite("edgeR")
the messages show everything is installed successfully but when I type
for example:
d <- readDGE (targets)
the…
updated 12.7 years ago • Guest User
I am analyzing RNA-seq data, and I have tried both the voom and robustified limma-trend approaches (following the process outlined in [RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR][1] and reviewing the user's guide), but the p-values do not agree very well. After adjustment, the robust limma-trend approach results in more significant transcripts than voom, and there is only mode…
updated 3.1 years ago • Tyler Sagendorf
div class="preformatted">Dear Vincenzo,
edgeR does use what can be viewed as a generalization of ANOVA, but
one
that is appropriate for count data. It does not use the...which
are
only for normally distributed data, and only for simple types of
experiments.
MDS in edgeR is not a sort of SSB.
Best wishes
Gordon
> Date: Mon, 1 Oct 2012 11:25:20 +0200
> From: Vincenzo Capece &l…
div class="preformatted">Dear List
I am a very starter in edgeR analyses.
When reading through the User Guide and homepage of edgeR, I didnot
find any examples of the importing data...I am writing to ask if someone can give me a small example of the
data that could be red in edgeR.
I would appreciate your help a lot!
Thanks
Li</div
div class="preformatted">Dear Franklin,
You don't say what version of edgeR you are using, but the latest
version of the User's Guide
http://bioconductor.org/packages/2.11/bioc/vignettes/edgeR/inst...of every case study.
You have to download these datasets for yourself. We don't ship them
with
the edgeR package.
Best wishes
Gordon
> Date: Sun, 29 Jul 2012 19:15:27 +0000
> F…
<div class="preformatted">Hello,
I am trying to repeat the edgeR process for section 3.3, 3.4 and 3.5
of the edgeR user guide.
However, in the edgeR data folder, labeled 'data', there are only four
.txt files. These .txt files are used to implement edgeR analysis the
SAGE experiment for sections 3.1 and 3.2 only.
Is it possible to receive the data files used to develop the...div class="p…
div class="preformatted">Hi edgeR community:
I'm testing for DE genes in two groups. Group A has 6 replicates,
group B
has 4 replicates. I spot a very strange...gene, that should be DE but
somehow
edgeR doesn't report it.
Here is the log2CPM of group A:
(5.8804275247607; 5.95666869234362; 6.24683910018322;
4.03634160591149...It's clear for us that these two groups has different CPM: B &g…
div class="preformatted">Dear all / authors of the edgeR package,
I have a question concerning the use of the multidimensional scaling
plot provided by the edgeR package.
I have
div class="preformatted">Dear Robin,
I don't think the problem is with edgeR. You are setting
genes=data[,0:1]
However there is no column 0, so 0:1 reduces to column 1, which is
being
set as annotation. But...just want:
y <- DGEList(counts=data)
Best wishes
Gordon
----- original message ------
[R] EdgeR annotation
Robin Mjelle robinmjelle at gmail.com
Sat Aug 24 13:50:55 C…
updated 11.3 years ago • Gordon Smyth
div class="preformatted">Dear all,
I use edgeR for differential expression analysis on a RNAseq dataset.
But I found that edgeR is very sensitive to outlier samples...NB distribution, and to estimate the dispersions.
Just wondering if there's an option available in edgeR? Or is there
any other RNAseq DE analysis package which is less sensitive to
outliers?
The outlier sample might be differe…
div class="preformatted">Dear Lucia,
This is a failure in the edgeR function estimatePs(), and it is
something
that I have never seen before.
Have you checked that your input counts are as...you expect? For
example,
summary(y$counts)
You don't say what version of edgeR you are using. Could you please
try
installing the devel version of edgeR, and tell me whether the problem
has
gone a…
div class="preformatted">Dear edgeR community:
In the output of edgeR for two groups testing:
topTags(et, n=20), for example.
We have:
Gene ID logFC logCPM pValue
div class="preformatted">Hi list,
Just a question regarding edgeR and dataset processing/filtering prior
to
calling differential expression.
Case Study 12 (RNA-seq of Hormone-Treated...LNCaP Cells) from the edgeR
manual mentions that:
"We filter out lowly expressed tags and those which are only expressed
in
a small number of samples...per million in at least three samples."
Then in section…
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 sessionInfo()
output?
The current version of edgeR is 3.6.1, whereas...My data is exactly count data, which are integers. I got the same
> results after I updated R/edgeR and rerun the code.
>
> I have some questions rel…
div class="preformatted">I see that the new version of edgeR has roast and camera implemented.
Is there a plan to implement romer in edgeR as well?
Thanks!
Julie
Julie Leonard
Computational
Recent ...
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