i found that the fold change of different RNAseq expression analyse results in edgeR is logFC, log2FC is also often used in other analysed ,i want to know if the logFC is same as log2FC in edgeR ,or it is based
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I'm new to edgeR and trying to perform differential expression for my samples, but having difficulties getting started. I have 8 pairs
Hello,
<span style="line-height:1.6">the edgeR manual (i.e. user guide that was l</span>ast revised 25 September 2014<span style="line-height:1.6">) explains very nicely...Hello,
<span style="line-height:1.6">the edgeR manual (i.e. user guide that was l</span>ast revised 25 September 2014<span style="line-height:1.6">) explains very nicely, with
Hi everyone!
I'm using edgeR to analyze a dataset with two treatment groups, each with three replicates. I've followed the canonical glm functionality...Hi everyone!
I'm using edgeR to analyze a dataset with two treatment groups, each with three replicates. I've followed the canonical glm functionality pipeline. Below is the code thus far. The problem lies in finding differentially expres…
questions:
Why are the logFC values all negative?
Am I doing something wrong?
```r
library(edgeR)
library(limma)
x <- read.csv("sample_matrix_rawcount_Tg.csv", header=T, stringsAsFactors=FALSE, row.names=1)
x <- data.matrix
updated 3.2 years ago • Gitanjali
Hello,
I would like to use only the lib size as normalizing factor in edgeR, so I am doing this:
<pre>
cds <- DGEList(counts = counts, group = group, norm.factors = MyNormFactors)</pre>
I __skip__ the ...Hello,
I would like to use only the lib size as normalizing factor in edgeR, so I am doing this:
<pre>
cds <- DGEList(counts = c…
updated 6.0 years ago • Udi Landau
regarding data cleaning and integration I find it hard to understand the statistics behind e.g. edgeR (If there are any recommendation (papers e.g.) to better understand these feel free to recommend some).
__Why this question...to see the effects of the prior df on my data, for which I used the following code:
<pre>
library(edgeR)
# loading data
groups <- as.factor(c("group1",…
div class="preformatted">Hi,
i am analysing a two-factorial RNA-seq experiment with edgeR. The
design of my study has two factors, genotype and treatment.
Genotype has three levels (A,B,C), "treatment" has two levels
plate-based) and to identify differentially expressed genes between clusters, I have made use of edgeR.
The input data was expected counts from RSEM and the example workflow is as follows:
all_edger <- DGEList(counts=all_expc
nbsp;Which would be the best way to get rid of unknown noise and find DE genes ?
<pre>
library(edgeR)
rawdata <- read.delim("selected_raw_count_matrix.txt",header=T,row.names=1)
y <- DGEList(counts=rawdata)
y <- calcNormFactors
case and multiple (6) controls. I am a non-statistician and am somewhat new to the minutiae of edgeR.
I include the core of the code below. Essentially I want to confirm whether the solution currently being used
updated 8.3 years ago • gavin.oliver
in expression and genes with similar expression across subjects. I looked at the example 3.5 in the EdgeR User Manual. I fit using the QL framework two models:
model1 <- model.matrix( ~ pattern + batch\_effects)
model2 <- model.matrix
updated 6.8 years ago • BharathAnanth
I am working with two subtypes of immune cells. For each of them I have two states - naive and activated. I am interested in the differential expression between these states in each cell type. I'll call these comparisons Contrast A and Contrast B. I am also interested to find out what is the difference between these two contrasts, i.e. to "compare the comparisons" (an illustration can be found he…
Deseq and EdgeR developers and user hi,
I'm testing an RNA-Seq data set for few developmental time-points (t0,t4,t12,t18,t21,t24,t48) with...Deseq and EdgeR developers and user hi,
I'm testing an RNA-Seq data set for few developmental time-points (t0,t4,t12,t18,t21,t24,t48) with no...expect that as compared to "t0", most genes will be under-expressed in "t4". Yet, as far as I read, EdgeR and De…
I am working with edgeR to perform some differential expression work. EdgeR has been a dream to work with and I have quickly reached the point
updated 9.0 years ago • mbio.kyle
hi,
i'm looking for some guidance on experimental design in EdgeR. The manual and examples i can find just dont cover what im looking for and im really stuck.
My experimental design is...hi,
i'm looking for some guidance on experimental design in EdgeR. The manual and examples i can find just dont cover what im looking for and im really stuck.
My experimental design is set up like this.
&…
updated 8.3 years ago • bpshiel
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
>...the
> linear regression on the batch factor? Can I then then feed the
> residuals into edgeR linear modeling? I want to compare how much…
updated 10.7 years ago • Gordon Smyth
<span style="line-height:1.6">Hi,</span>
I created a count table file using easyRNASeq and I am using edgeR downstream for the analysis. I want to create a rpkm-transform file from this but I am hitting a situation where when I...style="line-height:1.6">Hi,</span>
I created a count table file using easyRNASeq and I am using edgeR downstream for the analysis. I want to creat…
updated 9.6 years ago • Sylvain Foisy
Hi all,
I'm looking for some help when analysing RNA-Seq data for differential exon usage/splicing. I've previously used edgeR for DE analysis and was happy to see diffSpliceDGE as part of that package. What I don't know is:
1. how to obtain exon level counts
2. whether there is a normalisation step involved like there is in a DGE pipeline (i.e. TMM)
For the first point, I have BAM file…
updated 3.9 years ago • oakhamwolf
mouse, mm10, raw fastq-files). I imported the generated quant.sf data files into R for use with edgeR, following the manual here: https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html...txi.salmon <- tximport(files, type = "salmon", tx2gene = tx2gene)
head(txi.salmon$counts)
#edgeR import
cts <- txi.salmon$counts
rownames(cts) &…
Hello,
I am trying to use contrasts with a cell means model in EdgeR to compute log fold changes. I am a little confused by the results I get by modifying weights of the contrasts. For instance...Hello,
I am trying to use contrasts with a cell means model in EdgeR to compute log fold changes. I am a little confused by the results I get by modifying weights of the contrasts. For instance, I modi…
updated 7 months ago • pl23
treated with compound A with 0, 1, 2 mM for 0, 1, 2 hours, and you want to do DGE analysis using edgeR. You want to answer the question "which genes are differentially expressed in response to compound A": after taking into...and don't care about disease condition, time of treatment, not even \[A\].
How do you do it in edgeR?
In R, assuming the log(expression) being normally distribut…
updated 7.5 years ago • mousheng xu
Hi,
I have a question, we have generated pilot gene expression data with one sample per condition per subject. I am using `edgeR` package in R by following manual (`2.12 What to do if you have no replicates`). I have a control (baseline) sample followed by 5 different samples. I see that the below code tries to compare only two samples at a time (**R Code: Two samples at a time** - for instance;…
updated 2.3 years ago • mohammedtoufiq91
I'm analysing an RNA-Seq datasets with edgeR and using calcNormFactors to estimate normalisation factors. In one of my experimental groups all samples have normalisation
updated 6.4 years ago • maltethodberg
is simple: can we use/trust differential expression analysis (fold change, p-value) from DESeq2 or edgeR for these rRNAs? Especially since it is such very highly expressed.
__EDIT: __I am working with bacterial transcriptome
updated 6.7 years ago • r.aprianto
want to know which miRNAs are differentially expressed between these two groups.
Which approach of edgeR should I use?
The classic one with exactTest function or the GLM approach. <span style="line-height:1.6">What's the difference
updated 9.6 years ago • adrianna-christina
I am running edgeR on sRNA-seq data with two tissues Control(Tissue\_1) and Treated(Tissue\_2) having normalized TPM (transcript per million...value in the numerator and Control(Tissue\_1) in the denominator but the results I am getting with EdgeR are there with opposite sign (-ve sign in place of + and vice a versa); e.g.:
edgeR input:
<table border="0" cellpadding="0" cellspacing...tr>
…
div class="preformatted">
Hi All,
I had been trying to do DE analysis of my RNAseq experiment using
edgeR and am having some isssues. The details of the Experiment and
the R code I tried below:
(a) Paired experimental design with...Phenotype 1 and 2 upon treatment taking
into account the paired design
The R code tried:
library(edgeR)
counts<-read.delim(file="counts.dat",header=T)
pa…
Dear all,
I am new using edgeR to compare two samples, each of which has three replicates. My code is as follows. However, I found that if ommiting
updated 8.2 years ago • biolab
This has been bothering me AND I have seen conflicting information. When it comes to edgeR, how am I supposed to be analyzing the BCV plot to measure up my experimental design? Is it matter of what my BCV hovers...This has been bothering me AND I have seen conflicting information. When it comes to edgeR, how am I supposed to be analyzing the BCV plot to measure up my experimental design? Is it ma…
updated 4.0 years ago • science555111
I got interested in edgeR's capability of dealing with low counts and came across an error which turned out to be non-reproducible if you follow...1.077855e-07
design = model.matrix(~factor(rep(c("A","B"),each=3))`</pre>
Now if you run edgeR's base function for estimating tag wise dispersions
<pre>
dispCoxReidInterpolateTagwise(y=counts, dispersion=1.077855e...the matrix. ``
<…
Hi there,
I am wondering whether it is OK to use **`edgeR`**'s `glmQLFTest` on a model matrix with "successive differences contrast coding" as generated by `MASS::contr.sdif`. If that...sure this works the same way with successive differences.
NB, I have seen the instructions in the edgeR user guide for setting up custom contrasts. But I think (correct me if I am wrong) this does not help me h…
updated 17 months ago • Hannes
this? Sorry for all the questions, I'm just having trouble visualizing it. I just ran \`edgeR\` on a dataset with 3 control replicates and 3 experimental replicates. I'm not sure how the p-values and the FDR values
updated 7.8 years ago • jol.espinoz
div class="preformatted">Hi!
The edgeR manual is quite nice, but I'm not quite sure if I'm on the
right track..
The question to answer is: "Is there any significantly...TRUE);
targets <- data.frame(files=files, group=status,
description=description);
library(edgeR);
d <-
readDGE(targets,path="/Volumes/timemachine/HTseq_DEseq2",skip=5,commen
t.char="!");
colnames(d)
<-(c("…
Hello,
Thanks for the awesome tool. We are using edgeR for the RRBS for differential methylation analysis on multi regional tumors.
One of our purpose is to find out if there...for regionA and one library for region B in a tumour.
I see you have some suggestions to run EdgeR when there is no replicate but I am wondering how it should be performed for the methylation data, not gene expression
updated 8 months ago • annasoudi
Dear All,
I am new to multifactor analysis with edgeR, I have the following 12 samples (4 conditions and 3 replictaes)
<table border="1" cellpadding="1" cellspacing="1" style="width
updated 7.3 years ago • Paolo Kunderfranco
Hi,
Since edgeR appears to be designed to deal with count values, I was wondering if it could be applied to roughly detect differences
updated 2.4 years ago • eliza_3176
Hi edgeR authors，
I would like to apply the norm.factors calculated in gene expressions by using edgeR pipeline to other expression
updated 5.0 years ago • 2002ymx02
bias effect by RNA compostion. And DESeq2 prodvide counts(dds, normalized=T) to do this.But edgeR do not provided the similar function. The cpm(dds, normalized.lib.sizes = TRUE) fucntion divided by the product of library...bioc/vignettes/DESeq2/inst/doc/DESeq2.html count transformation part) So can I deem that cpm() in edgeR and vst()/rlog() is do the same extent of normalization in some way,bec…
updated 5.1 years ago • 15958021290
Enter the body of text here
Code should be placed in three backticks as shown below
```r
# include your problematic code here with any corresponding output
# please also include the results of running the following in an R session
rep <- tximport(files, type =
"salmon",countsFromAbundance="scaledTPM",varReduce=F, txOut =
F,tx2gene=tx2gene,ignoreTxVersion = TRUE)
>…
updated 3.8 years ago • Themis
Hi,
I'm trying to figure out which is the best model to go with in an experiment, so I'd appreciate any advice people can give, as I'm essentionally a wet lab person.
I'm aiming to find genes that associate with changes in triglyceride levels (TG) in the liver samples.
I used featureCounts to summarize the gene level.
```
> dge <- DGEList(counts=expr)
> keep &…
Hi,
I have been trying to load edgeR on my laptop with Windows 10. This is what I get after typing the 2 recommended lines into my command window, and then copying
updated 7.9 years ago • nancyjwahl7
Dear edgeR user community,
I have RNA-seq data downloaded from TCGA from 7 patients, both lung tumor and normal samples. At first...Dear edgeR user community,
I have RNA-seq data downloaded from TCGA from 7 patients, both lung tumor and normal samples. At first I used edgeR with the GLM approach to account for patient differences, but the logFC values seemed too small. Min and max are -1.03 and…
Thanks in advance for any help someone more experienced with edgeR and DE analysis can offer.
I am new in a lab doing this kind of work and I have only been working in R for about a month. My team...tells me this code performs differential expression analysis of two groups via a t-test and edgeR's Exact Test. We also report both sets of results in presentations of the analysis. This was my fi…
updated 5.0 years ago • acs1990
doc/de.html)
thought that I could ask you please :
**would the same pipeline (that includes edgeR or limma) apply to scRNA-seq data from Drop-seq/10X Genomics ?**
given the fact that the number of UMI reads per gene is very
updated 5.2 years ago • Bogdan
I am working on RNA-seq data with multiple experimental factors and I
am
trying to reproduce the edgeR manual, chapter 3.2.3, GLM approach.
> design <- model.matrix(~0+group, data=y$samples)
> colnames(design) <- levels(y$samples
Hi,
I am analyzing mRNA-Seq dataset using `EdgeR` package, I have question while extracting co-efficient comparisons after fitting the model (example below). In `limma...lt;- model.matrix(~0+Culture_Types)` with `corfit` (as below), however, doing this first time time `EdgeR`.
corfit <- duplicateCorrelation(df, design, block=sample_ann$Pt)
fit <- lmFit(df,design,block=sam…
updated 21 months ago • mohammedtoufiq91
Hi,
I have an RNA-seq experiment that is similar to section 3.5 in the edgeR user’s guide, i.e. a nested paired approach, and I have used this approach to analyze my own data. Briefly, the experiment
updated 9.6 years ago • Mauve
I'm pretty new to RNA-seq data analysis. I want to do the TMM normalization on my RNA-seq data using EdgeR package in R. I have two questions:
1) How can I convert .fastq files to .txt files to be able to feed them into the EdgeR package
updated 8.8 years ago • hamidrezarazzaghian
While I'm using edgeR how can I convert a .txt file and .tabular file into .RData file?
please provide a code to completion of the process
updated 3.5 years ago • abhisekdey061
to make two pairwise comparisons, A vs B and B vs C. I have 1000 genes.
I can provide contrasts to edgeR/DESeq2 for each of the pairwise comparison, thus I will have two contrasts.
The first time I test A vs B, I will have a list
<div class="preformatted">Hi List,
I just want to know how to output the graphs generated during edgeR
analysis to pdf file. Any help would be really appreciated. Thanks in
advance.
Thanks,
Jung
[[alternative HTML version deleted...div class="preformatted">Hi List,
I just want to know how to output the graphs generated during edgeR
analysis to pdf file. Any help would be reall…
updated 12.4 years ago • Javerjung Sandhu
Hi,
I try to do differential expression analysis by "EdgeR", I have the "counts.csv " which achieved by "HTSeq". i want to add the "symbol" column with the gene symbol corresponding to...Hi,
I try to do differential expression analysis by "EdgeR", I have the "counts.csv " which achieved by "HTSeq". i want to add the "symbol" column with the gene symbol corresponding to the...Gene ID t…
updated 4.8 years ago • alihakimzadeh73
div class="preformatted">Hi all,
I have some questions regarding multi-factor-glms in edgeR. I am
working on a RNA-seq experiment:
I have 24 samples from 3 "treatments" each having two levels. This
means 3 biological...condition
"pop" from the model?
Hope this code demonstrates what I mean:
## CODE start
library(edgeR)
## generate a df of neg. bionm. counts
y <- as.data.frame(matri…
Hi,
I'd like to be able to use EdgeR to look for allele-specific differential expression in data sets containing NAs for some samples. The analysis
I have an experiment where I have two groups (control and disease). In my control group, n=5 and for the disease group, n=10. Within each group I have measures over time (0, 24, and 48) and so n=15 for control and n=30 for disease. I am trying to design a design matrix in edgeR to test for change over time in each group (C0 vs C24, C0 vs C48, and C24 vs C48 and the same for disease group), and ch…
updated 3.9 years ago • Hajar
I have searched this forum, and found some threads (https://support.bioconductor.org/p/83811/, https://support.bioconductor.org/p/103623/ ) on this topic but don't resolved my problem. According to the discussion, this problem is caused by the old version of g++ library. However, in my case, the error remain with g++ version 4.9.2, which is said to support c++11. I am testing g++ version 5.5.&…
updated 6.0 years ago • Pengcheng Yang
div class="preformatted">
I am working my way through the edgeR User's Guide and following
section 3.3, I encounter a problem. I run the following commands -
using my own counts data:
## Chapt
bypass its
estimateGLMCommonDisp, estimateGLMTrendedDisp, estimateGLMTagwiseDisp steps in edgeR? or is there way to use dispersion from 30 biological replicates as a prior?
2) If so, I was wondering if I can replace 
updated 10.0 years ago • lwc628
Hey guys, I need some help regarding using edgeR in CRD w/ factorial arrangement experiments. The main problem here is to fit the group/design into the linear model.
To...that, analyze main factors interactions or if they act together on each gene in each organ/timepoint.
edgeR approach used: Experiments with all combinations of multiple factors
The groups:
```
[1] CM.14.NO CM.14.NO CM.14.…
updated 7 months ago • tsl0026
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