Hi Guys,
I have used edger and R to get the top gene-list that are up regulated and down, and I am able to export the list of genes significantly differentially...anyone help me on this how to separate each file with a list of up and down regulated genes using Edger and R.
Thanks a million
San
 
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So the only different factor I have
is the genotype.
I am trying to analyze the data with the edgeR package, however I am
not
sure if I can use the GML function for multiple testings or how should
I
made my design matrix
Hi,
I'm having trouble setting up a edgeR design matrix for an RNA-seq dataset I've been working with. We have a number of subjects, with each subjects having 1 - 7...Hi,
I'm having trouble setting up a edgeR design matrix for an RNA-seq dataset I've been working with. We have a number of subjects, with each subjects having 1 - 7 samples...to compare responders vs. nonresponders, but I'm …
updated 4.5 years ago • jcrowdis
<div class="preformatted">Dear Josquin,
Thanks for providing some data. We've confirmed the problem is that
the
glm functions provided with R fail to converge, when used to fit a
negative binomial glm, to some of the rows in your data, especially
rows
with very large counts. The problem affects glmFit and glmLRT, as
well as
estimateCRDisp, because they all make calls to glm.fit.
We're w…
div class="preformatted">Hi all,
I am using DESeq2 and edgeR to perform DE analysis on paired samples
on a dog cancer project.
Sorry if the question is redundant but I can?t find one
to normalize all of the data, which is
implemented in the function calcNormFactors from the package edgeR,
but I
don't understand how can I put the read counts into a matrix since my
files
contain different numbers of genes (rows
updated 11.4 years ago • Jan Zaucha
using DRAM + RAST) across my species of archaea.
Therefore one of the apps is DESeq2 or edgeR. While these packages were initially designed for transcriptomics, I was wondering if it was possible to feed it a matrix
org.Mm.egENSEMBL) to annotate the differential expressed genes (tophat(mm9)-featureCounts-RUVseq-edgeR). Although the results are nice some genes could not well being annotated and I guess it is is because I am using a GTF (NCBI37
Hi,
I am trying to decide on the best design for my EdgeR differential-expression analysis. I have RNA-seq data from four patients - matched blood and liver for three of the patients
updated 4.2 years ago • Lucy
b/w genes (as opposed to across conditions for
>a given gene) is not a standard use case within edgeR (yet) and
>there are a number of issues that should be dealt with if you want
>to do this well. I'm sure others on the list...there are a variety of issues that hinder these comparisons.
Thanks so much!
Jenny
>That said, edgeR has fairly general routines to analyze …
<div class="preformatted">Hi All,
I was wondering if anyone had any idea how one might
put error bars on the log fold changes calculated by edgeR? I'd like
to do this so I can show examples of differentially expressed genes on
a bar plot, and show them in comparison to...wondering if anyone had any idea how one might
put error bars on the log fold changes calculated by edge…
div class="preformatted">Hello all --
I am using edgeR to analyze RNASeq data. Thank you so much for this
software and the clear and straightforward user guide. I have a
question...design matrix and call
contrasts to either compare each tissue to the average of the other
two (e.g., edgeR section 3.4.3-4) or perform pairwise comparisons
between tissues while including subject (e.g., edgeR se…
updated 11.5 years ago • Findley Finseth
Hi!
I was wondering... how do you specify edgeR that you want to obtain only the DE genes in Treatment B compared to Treatment A and Controls. I thought about using the
ENSG00000231949.1" "ENSG00000162510.5"` total 61471. How can I convert these ids to refseq ids for edgeR analysis? I have tried several ways but failed each time.
`gids=mapIds(org.Hs.eg.db,keys = rownames(y1),keytype = 'ENSEMBL
div class="preformatted">I am analyzing a set of RNA-Seq data without replicates, possibly
using edgeR. (We understand limitations and are only interested in
descriptive analyses.) There are three different treatments...CAA62189.1| 173
> dge<-DGEList(count=reads)
>y<-cpm(dge,prior.count=2,log=TRUE)
> head(y)
…
Hi BioC community,
<span style="line-height:1.6">I have spectral count data (proteomics) to analyze. I have two groups (A ad B) to compare with 8 patients by group. Each sample was processed in duplicate, leading to 16 distinct patients in the study and 32 samples (16 by group).</span>
As for the method to use to detect differentially expressed proteins between the two groups, I rea…
updated 9.2 years ago • eleonoregravier
Hi,
I am new to bioinformatics. I use EdgeR. I analyze a study in humans with 3 factors, each having about 5 levels. Can this pose a problem for modeling for differential
<div class="preformatted">Hello!
I have been struggling with one of the skeletal muscle biopsies in my
study. The RNA quality is very good and looking at tissue specific
gene
expression they are all there, although some with very different
values
for some genes compared the other biopsies.
Please see the attached plots using edgeR. The gof() calculation gave
0
"TRUE" in the $outlier table.…
expression on GO terms. Expression of each GO terms is sum of gene expression in this GO. Can I use edgeR to compare GO expression between two conditions?
Thanks!
__UPDATES:__
Thank you all for suggestions and comments.
Sum
Hi,
I wanted to estimate the dispersions for RNAseq dataset using the robust version in edgeR package. After running following line of code I got an error in recent version of edgeR/Bioconductor despite the fact...that identical code work on the same dataset in previous version of edgeR/Bioconductor:
<pre>
dge <- estimateGLMRobustDisp(dge, design=moma)</pre>
Error in .compr…
Hello,
I'm trying to analyze a dataset in which there are **repeated measures** using **edgeR**.
I have 48 RNA samples, collected from 16 subjects (3 time points: T0, T1, T2): 8 subjects belong to the group placebo, and the...Hello,
I'm trying to analyze a dataset in which there are **repeated measures** using **edgeR**.
I have 48 RNA samples, collected from 16 subjects (3 time points: T0, T1…
updated 13 months ago • greta
Hi
I am using edgeR for differential gene expression analysis. The following command :
> summary(de <- decideTestsDGE(lrt.CHvsH))
gives
updated 9.1 years ago • p_das
Hello,
I am trying to analyze my data based on section 3.3 of edgeR and I got stuck in the fist part
design <- model.matrix(~0+Group)
colnames(design) <- levels(Group)
fit <- glmQLFit...Hello,
I am trying to analyze my data based on section 3.3 of edgeR and I got stuck in the fist part
design <- model.matrix(~0+Group)
&…
updated 7.0 years ago • Mahnaz Kiani
I have a list of gene of a specific gene ontology and I would like to extract the fold change from EdgeR object based on the list of genes.
how is it possible to be done?
is it possible to use EdgeR for it?
thank you for your help...code and extracted the gene of GO i am focusing on:
```
#Load the required libraries
library(edgeR)
library(limma)
library(RColorBrewer)
library(mixOmics)
library(HT…
updated 3.2 years ago • najib
I have gone through HTSeq-counts and then I have done differential expression gene analysis through EdgeR, DESeq, and DESeq2.
My pipeline is:
Tophat2 > HTSeq count > EdgeR, DESeq, or DESeq2
Samples: Control: Control\_rep1; Control...is it not advantageous to use Log2 fold change values to generate heat maps with DESeq, DESeq2, and EdgeR results? If anyone could clarify this. Asid…
Hello alll. I am a newbie in bioinformatics and still learning.
The thing is, I want to do differential expressed gene(DEG) analysis in the TCGA RNA-seq data.
DESeq2 and edgeR manuals said they require __raw count data__ as input, so I downloaded _STAD.rnaseqv2\_\_illuminahiseq\_rnaseqv2\_\_unc\_edu\_\_Level\_3\_\_RSEM\_genes\_\_data.data_
form \[FireHose\] (http://gdac.broadinstitute.org/) an…
effect (GD vs WT) within untreated
Is my `res_GD_vs_WT_within_untrt` correct?
I have gone through [edgeR user guide][2] as well as [A guide to creating design matrices for gene expression experiments][3], yet I am asking these questions...p/126346/#126374
[2]: https://www.bioconductor.org/packages/devel/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf
[3]: https://www.ncbi.nlm.nih.gov/pmc…
div class="preformatted">
I'm just wanting to confirm my understanding of the edgeR topTags()
output. I'm using a design matrix with many coefficients (76
genotypes, 2 treatments[sun, shade]).
1) In the topTags
Hi all,
I have a question about edgeR Bisulfite sequencing and differential methylation analysis. I'm following the main manual 'differential analysis
updated 14 months ago • Krzysztof
out the down-regulation.
I created a DGEList object and then set normalization factors to 1 (using edgeR's calcNormFactors function with method "none").
My question now is if there is still normalization by total library size...by applying the voom function and proceed as usual ... (or also alternatively analyze the data using edger). Or would I have to provide custom scaling factors to correct…
updated 6.8 years ago • biominer
div class="preformatted">Hello Bioconductor mailing list,
I'm using edgeR to analyze RNA-seq and RIP-seq data. I'm using the
moderated gene-wise dispersion method where I choose a prior.n based
Hey,
Is it possible to correct for both a location and batch effect using Limma?
I have 4 surfaces: PET, PE, Glass and Water,
5 locations: A, B, C, D ,E,
and 2 batches: 1, 2
enter OTU<-read.csv("filterotu.csv",header=T,row.names=1)
targets<-read.csv("sample.csv",header=T,row.names=1)
tax<-read.csv("filter_tax.csv", header=T, row.names=1)
t…
updated 3.8 years ago • Katherine
When I am applying these two different designs in edgeR GLM test it gives different results:
design<-model.matrix(~0+treatment:group+group:plant,data=y$samples)
design <...When I am applying these two different designs in edgeR GLM test it gives different results:
design<-model.matrix(~0+treatment:group+group:plant,data=y$samples)
design <- model.matrix
updated 7.7 years ago • simarsidhu25
I'm doing some DGE analysis with 4 groups! I have tried to use the glmQLFTest as suggested in the edgeR users manual, but there are barely any differently expressed genes with FDR < 0.99. On the other hand for the same comparisons
updated 8.2 years ago • grastalt27
gt; y$genes <- fc$annotation[, "Length", drop=FALSE]
How can I add `` rawCountTable `` into `` edgeR `` and tell it that the first column represet the `` y$genes ``?
Thank you in advance
updated 7.0 years ago • mictadlo
div class="preformatted">Dear All,
I am using edgeR for an RNASeq experiment (~30 samples), where I need
to
explore the influence of 2 factors with 2 levels each (there are
actually
data-set and
goals.
I was wondering if anyone can give me a feeling on when is better to
use
Voom vs EdgeR (or DESeq) and whether modelling the distribution is
really
that important vs just modelling the variance.
My data set
The results shows a big difference between the amount of differential bound regions identified with edgeR or DEseq2(with 98% less peaks identified by DEseq2 in respect to edgeR). What is the reason behind such difference? Which
updated 18 months ago • Giulia
Hi,
I am trying to decide which covariates I should include in my model for EdgeR. To do this, I have read that I should compare a full model including the covariate and a reduced model that lacks the covariate...using a likelihood ratio test. How would I go about this in EdgeR and what metrics should I use to decide whether to include the covariate (e.g. patient age) or not.
Many thanks!…
updated 4.2 years ago • Lucy
<div class="preformatted">Hi,
Attached is the input file that I used to run EdgeR for my data set.
Ideally the input file should be able to run through the following
R-script:
*library(cluster)*
*library(gplots...div class="preformatted">Hi,
Attached is the input file that I used to run EdgeR for my data set.
Ideally the input file should be able to run through the following
R-script…
Hi,
I am trying to perform differential gene expression analysis with edgeR. I have four conditions T1, T2, T3 and T4 and two batches. I am running the following codes:
Count1=read.table("GENESFORANALYSIS.txt...differentially expressed genes?
I would like someone to kindly reply to me. I have checked the edgeR manual and not able to understand it.
Thanks a lot.
Arumoy
updated 4.0 years ago • chatterjee.arumoy
Hi sorry for the random question. I was using edger and used: "fit <- glmQLFit(y, design) " followed by: "lrt <- glmLRT(fit, coef=6) " instead of using glmQLFTest and got some
updated 6.5 years ago • Catalina Aguilar Hurtado
a few Bioconductor packages into R. I have R version 3.3.3 and it does not allow me to install edgeR because it says an new version of R is required. I also get this message Update all/some/none? [a/s/n
updated 4.3 years ago • yassiflower
This question is split into 2 parts:
(1) __Can TMM normalization through edgeR be used for other count data like OTU counts and contig counts? __
(2) A__fter you calculate TMM, would converting...This question is split into 2 parts:
(1) __Can TMM normalization through edgeR be used for other count data like OTU counts and contig counts? __
(2) A__fter you calculate TMM, woul…
updated 7.4 years ago • jol.espinoz
of text here
Code should be placed in three backticks as shown below
```
library(limma)
library(edgeR)
directory="/home/abhisek/Downloads/result analysis"
filess <- grep("a_gene_count_matrix.txt",list.files(directory
but in this case I would be grateful if you could point me to the
right
answer
I am using edgeR for DEG analysis of SAGE tags and I noticed that,
when
using tagwise instead of common dispersion, the number of
differentially
to see differentially expressed genes between two
samples, each with three replicates. I am using edgeR to do the
analysis. However, when I am running the exactTest using the following
command, I am getting an error.
FM_HCV1_HCM1.exactTest2
We have a multi-factor RNA-Seq experiment with multiple baseline measures that we would like to model using edgeR:
* 2x pre-treatment samples per mouse \[time=0\]
* 1x post-treatment sample per mouse \[time=1\]
* 2x treatment groups (all mice are treated...factor RNA-Seq experiment with multiple baseline measures that we would like to model using edgeR:
* 2x pre-treatm…
updated 8.3 years ago • gatk
Hi! I'm new with edgeR and Differential Expression analysis in general so I'm having some trouble designing the analysis for my single-cell...Hi! I'm new with edgeR and Differential Expression analysis in general so I'm having some trouble designing the analysis for my single-cell RNAseq data.
First of all, my input is a count matrix in a txt file with genes in rows, cells in columns, and exp…
Hi
I am new to edgeR, and I don't have a basis so much in R programming since I used to work with python for my analysis. The counts that achieved...a GLM. Although I have to identify DE genes by using log2 fold change and likelihood (LR) test in edgeR. I write code like below for the beginning :
library(edgeR)
directory="/home/ali/Desktop/SAMPLES1/"
files <-grep("coun…
Hi
I would like to determine the differential expression of some of the selected genes from the plot I obtained in edgeR DE analysis. Are there any plots which we can construct which would depict the differential expression of a single gene...to determine the differential expression of some of the selected genes from the plot I obtained in edgeR DE analysis. Are there any plots which we can con…
updated 7.0 years ago • fawazfebin
am conducting differential abundance analysis on some metagenomic data. In comparing the results of edgeR and DESeq2, I find that there are drastically more differentially abundant tags found by DESeq2 compared to edgeR (n...59 vs. 17, both FDR < 0.05). Further, only 10 out of 17 of edgeR's significant tags overlap with those found by DESeq2. Does anyone know why such a discrepancy would o…
updated 6.8 years ago • audrey.o.renson
Hi, I would like to apply edgeR TMM normalization without converting data format into "DGEList", in other words I would like to manipulate the raw count...I ask that if I just do the following:
<pre>
(Raw count table)*(norm.factor), where
norm.factor=edgeR::calcNormFactors((Raw count table),method='TMM').</pre>
And then conduct downstream analysis. Does this procedure make sense
updated 7.6 years ago • wt215
Hi,
I understand that, under edgeR, the __dge$AveLogCPM after estimateGLMCommonDisp__ gives the same result as doing __aveLogCPM(data, lib.size = dge
Hi
I doing DE analysis using edgeR. I have 12 paired samples from human blood cells. 6 treated with drug and 6 untreated. After doing DE analysis I get mostly
Dear Community,
i have just started edgeR properly today. I have a dataset of 59 spatial replicates of one soil type (plot scale). Analysis yielded that 9 of those...analyses (DESeq, ANCOM, some non-parametric t-test and anova variations), but i really want to get edgeR to run for comparison.
I followed tutorials in the vignette and [here.](https://bioinformatics-core-shared-training.github.io.…
updated 6.6 years ago • trichter
<div class="preformatted">Dear Gordon,
I am very interested in "Comparisons Both Between and Within
Subjects" of edgeR. Because one of my study is according to this
design. But i found some detailed analysis have not been provided in
the manual...Dear Gordon,
I am very interested in "Comparisons Both Between and Within
Subjects" of edgeR. Because one of my study is according to this
desig…
I have followed this [tutorial](https://f1000research.com/articles/5-1438/v2) for edgeR. On this [side](https://toolshed.g2.bx.psu.edu/repository/display_tool?repository_id=f599adf23b671cad&tool_config...when I have created the following files:
1.
Differentially expressed gene file but edgeR does not appear to produce a tabular file with gene names in the first column, and TR…
Hello there,
I am trying to use roast in combination with edgeR glmTreat and an average RPKM filter, but I am not sure how to correctly implement this. Hope someone can help with this...Hello there,
I am trying to use roast in combination with edgeR glmTreat and an average RPKM filter, but I am not sure how to correctly implement this. Hope someone can help with this.
So our strategy is to use…
Hi,
I would appreciate some help to find out the correct design matrix for my experiment in EdgeR.
The experiment is about thermal acclimation in fish, where I have two groups 1.Control 2.Treatment. From each group...So my question here is **Is there any model close to nested ANOVA that fits to my experiment in EdgeR?** I looked for different possibility in the manual but most of them are cr…
Recent ...
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