Bioconductor Forum

Hi, Interested in using the nearestTSS function from edgeR, I was not able to reproduce the provided example with *Sus scrofa*. Here is the example with ```species="Hs"``` (default value), the

Sus_scrofa edgeR

updated 2.4 years ago • Jon

According to edgeR package, I can estimate the dispersion of my dataset using:     y <- estimateDisp(y, design, robust=TRUE)  &nbsp

r edgeR estimatedispersions coordinate

updated 8.8 years ago • pertille

I have been running an analysis of RRBS data using edgeR, following the guide in the edgeR manual. The metadata looks like this: <table border="1" cellpadding="1" cellspacing="1" style

edgeR rrbs

updated 5.7 years ago • ingerslev

have higher read mapping abundances than the same region for a different organism. I am wondering if edgeR, or any other differential expression software really, would be applicable for testing this hypothesis. I understand...challenges than mapping to genic regions, and this leads me to wonder if the approaches used by edgeR, such as the TMM normalization and the shrinkage of dipersion using an …

edger differential expression

updated 4.4 years ago • hollandademello

Hi, I'm doing differential analysis with edgeR. In that package goana function worked well for Gene ontology but kegga is giving some error. <pre> head(de) logFC unshrunk.logFC

edger r bioconductor pathway analysis kegg

updated 6.6 years ago • Biologist

analysis using Arabidopsis annotation as reference (available at ""org.At.tair.db""). I am using the edgeR package particularly the function __goana __however when I specify the species (species=At) the function doesn't recognize...the library org.At.tair.db. The coding is below, eny help would be much appreciated: <pre> library(edgeR) source("https://bioconductor.org/biocLite.R") biocL…

gene ontology

updated 6.6 years ago • jfreixas

Four doses - D0, D1, D2 and D3. There were no replicates. Total 12 samples. We are trying to use edgeR to identify differentially regulated genes. Since edgeR doesn't give p-values without replicates, we took samples coming

edgeR DOSE edgeR DOSE

updated 11.2 years ago • Sandhya Pemmasani Kiran

Hi all, I just started to use edgeR and I have a question related to the plotBCV funtion. When plotting the average low CPM vs the BCV (plotBCV), I get a plot...Hi all, I just started to use edgeR and I have a question related to the plotBCV funtion. When plotting the average low CPM vs the BCV (plotBCV), I get a plot where

rnaseq edger

updated 7.6 years ago • davide.bau

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

edgeR edgeR

updated 10.6 years ago • Guest User

Hi, I have a gene expression data in cpm not raw count and I want to do DE analysis using edgeR. In this case, is it okay to follow the overall workflow shown in the edgeR user guide because it's not raw counts in integer

edger

updated 4.4 years ago • ychoi18

Hello everyone: I am working on the RNA-seq data with edgeR recently. I tried to find which function normalizes the reads between samples and found that the "betweenLaneNormalization

edgeR

updated 21 months ago • 冠宇

average transcript copy number per given amount of (clean, non-junk) sequenced RNA bases." Would edgeR still be the appropriate package to find differentially expressed genes or should I turn to chip expression packages

edger rnaseq coverage

updated 8.4 years ago • bastien.chevreux

Hi , I'm trying to perform rrbs dme analysis using edgeR on 50 samples (5 replicates per timepoint /sex). It seems to be running forever (>8 hours) and not produce any output. Design

edgeR

updated 3.9 years ago • Archana

am wondering if it would be appropriate to include this contamination metric as an offset matrix in edgeR or glmGamPoi or DESeq2* (in addition to a library.size measure). Similar in concept to observation level GC corrections...but it doesn't seem easily done in existing differential expression models. I've seen in the new edgeR release that there's specific mention of incorporating log transform…

DESeq2 glmGamPoi offset edgeR scRNAseq

updated 12 weeks ago • Alec

in the contrasts of each of the treatments vs. the "siNT" control. I thought that the model of edgeR would be useful to score significant hits while at the same time dealing with the mentioned technical biases in a meaningful...feasible to try to adress a problem with a design that has so few genes and so many treatments using edgeR (or DESeq2)? library(edgeR) ## Data look similar to this: read…

edgeR edgeR

updated 10.3 years ago • Guest User

Hello, I am using edgeR to try to construct a model to compare multiple conditions from some sequencing data. I have three growth conditions...Hello, I am using edgeR to try to construct a model to compare multiple conditions from some sequencing data. I have three growth conditions (A, B, C) and replicate samples for each condition at time 0 (T0) and after so many generations (T1). The edgeR m…

edger anova sequencing

updated 8.6 years ago • kmyers2

Hi, Using DESEQ2 and EDGER in diffBind gives huge difference in total number of differentially bound sites around 8000 for DESEQ2 and around...700 for EDGER, reading the vignette, the number should be fairly similar. And also do we need to use "**DBA_SCORE_TMM_READS_FULL**" in **dba.count

diffbind

updated 5.2 years ago • dewshrs

Hi, I am using edgeR to analyze RNASeq data and I wonder about how the interactions between two factors is dealt with, especially when the...in my view, time does not play the same role on all genotypes, and yet the table tells me that edgeR does not find the interaction between factors significant. Is this because the cpms for those genes are close to 0 when

rnaseq edgeR edger main and interaction effects

updated 6.9 years ago • David Rengel

I am trying to use edgeR to analyse differential gene expression from my RNA-seq dataset.  The experimental design is as follows: I had 3...I am trying to use edgeR to analyse differential gene expression from my RNA-seq dataset.  The experimental design is as follows: I had 3 different...DE between group 1 and group 2 and between group 1 and group 3.  So I think I want…

edgeR differential expression rna-seq

updated 8.0 years ago • lynski008

unsure as to if there is any particular condition that is the deciding factor between whether to use edgeR or DESeq packages for differential expression analysis for RNA Seq data. For example, does it depend upon how the counts

edgeR DESeq edgeR DESeq

updated 11.9 years ago • Sakshi Gulati

<div class="preformatted">Dear edgeR users community, Good day. I'm analysing my RNA-Seq data which has 2 different genotypes (treeHS, treeLS) and time of treatment (0H, 3H, 24H, 96H) with edgeR. I would like to learn the differential expression of treeHS vs treeLS at specific time points i.e. 24H. Thanks to Prof Gordon and his colleagues, the latest edgeR user's guide (Chapter 3) is ver…

edgeR edgeR

updated 12.1 years ago • KJ Lim

<div class="preformatted">I'm trying to analyze an RNA-seq experiment where the PCA plot shows better clustering by the day the experiment was done rather than treatment type. Using edgeR to determine differentially expressed genes resulted in less than 5 genes with an FDR under 5%. Creating a GLM model to...plot shows better clustering by the day the experiment was done rather than treatme…

GO edgeR GO edgeR

updated 11.3 years ago • David O'Brien

Hi everyone, I am using edgeR to identify differentially expressed transcripts based on a simple RNA-seq setup (tumor vs control samples). The *DGELRT...object with results provided by edgeR contains, among others, logFC values calculated for the contrast that I used (Tumor vs Control). I additionally need the

edgeR batch-effect RNA-seq read counts ngs

updated 5.7 years ago • Roman

is a special case of the > negative binomial with zero dispersion. So, simply fit a model using edgeR > or DESeq2 with a separate coefficient for each group of technical > replicates. Thus all the experimental variation...I have used this method on a pilot dataset with several technical > replicates for each condition. edgeR said the dispersion was something like &…

Sequencing Alignment GO edgeR DESeq2 Sequencing Alignment GO edgeR DESeq2

updated 10.1 years ago • Gordon Smyth

Hi all, I have an experiment with serial sampling that I want to model (for e.g. presence of disease, disease severity). I want to know what the best way to go about this would be when doing differential expression analyses. My questions are: 1. **Can I handle repeated measurements using `edgeR`?** My understanding is no based on previous posts (e.g. https://support.bioconductor.org/p/1077…

edgeR limma variancePartition

updated 3.2 years ago • jackgisby

Of these 9 samples, 4 are control and 5 are treated, all male. I have gone through the full edgeR differential expression analysis pipeline and the full Ballgown pipeline as well but am running into the same issue...I will be focusing on edgeR with my question and code. My issue is that my analysis does not give me any Differentially Expressed Genes (DEGs) with...I was unable to embed several…

edgeR RNASeq RNASeqData Bioconductor

updated 19 months ago • Rebekah

Two tools give the adjusted p-values for multiple testing.  DESeq used Benjamin-Hochberg correction and edgeR uses FDR. According to wikipedia Benjamin-Hochberg is the same as FDR. So, the correction is the same, but the names are different...the adjusted p-values for multiple testing.  DESeq used Benjamin-Hochberg correction and edgeR uses FDR. According to wikipedia Benj…

deseq2 edger

updated 8.9 years ago • tonja.r

I have a paired test situation, (with and without treatment) on 8 samples. The experiment is (targets.txt): <pre> files Subject Treatment r1.txt 1 NO r2.txt 1 TREAT r3.txt 2 NO r4.txt 2 TREAT r5.txt 3 NO r6.txt 3 TREAT r7.txt 1 NO r8.txt 1 TREAT</pre> r1,r2,r3,r4,r5,r6 were sequence…

edger design and contrast matrix

updated 9.7 years ago • Son Pham

I'm using glmLRT() from edgeR to analyze some RNA-seq data. My experimental design has one Treatment factor with three classes (A, B and C), one continuous...I'm using glmLRT() from edgeR to analyze some RNA-seq data. My experimental design has one Treatment factor with three classes (A, B and C), one continuous Age covariate and one Batch factor with 19 levels. > colnames(desig…

edger contrast covariate glmlrt()

updated 7.4 years ago • Jeff Skinner

Dear All, I have a tricky question regarding the use of EdgeR in R to run differential expression analyses of the following experiment: it is a multifactorial experiment with...Dear All, I have a tricky question regarding the use of EdgeR in R to run differential expression analyses of the following experiment: it is a multifactorial experiment with around...3)Breed. Could you advice, which of…

rRDPData r

updated 2.4 years ago • Mohamed

at="" imb.uq.edu.au=""> > To: <bioconductor at="" r-project.org=""> > Subject: [BioC] edgeR: Identifying genes up regulated in one of > multiple samples, and those stable across samples > > Hi; > > I have a list...of similar genes etc. which is not a > problem for me - but will it effect the stats from edger as obviousl…

edgeR edgeR

updated 13.3 years ago • Gordon Smyth

div class="preformatted">Hi List, In the edgeR manual it is mentioned that the package may be useful in the analysis of other count based studies and I am wondering...sampling properties to when you are doing a DE study of gene expression. Hence I thought to use edgeR to do the analysis as it can normalise for both overall count numbers and the TMM normalisation for target tag complexity

edgeR edgeR

updated 13.0 years ago • josquin.tibbits@dpi.vic.gov.au

Hello How to get TMM normalized matrix from count matrix using edgeR I saw that edgeR guide recommend estimateDisp directly rather estimateCommonDisp -> estimateTagwiseDisp http...www.bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf And I confirmed that those results are different. Also, low number of DEGs(by exactTest...class <…

edger

updated 4.0 years ago • hyojin0912

readable by biologists, but understandable by bioinformaticians. Preferably related to DESEq2 or edgeR NGS data analysis pipelines   Regards Vladimir

deseq2 edgeR

updated 7.0 years ago • Vladimir Krasikov

shown above, the function takes as input a tr object, a list of DEGs, which, in a edgeR pipeline, appears similar to this (just random data to show what the format looks like): Length Symbol logFC logCPM F PValue...Since, apparently, goana (belonging to the package limma) isn't designed specifically for edgeR, ***I'd like to run goana on a DESeq2 DEGs list provided externally. However, i…

DESeq2 edgeR goana GO

updated 2.5 years ago • Raito92

I want to do gene DE for my cohort (40 cases vs 20 controls) with several covariates (age, sex, subject, RNA integrity number) in edgeR. However, I get the following warning in estimateDisp step (see below). I have read the edgeRNA manual and I assume this is...40 cases vs 20 controls) with several covariates (age, sex, subject, RNA integrity number) in edgeR. However, I get the following warnin…

edger R limma

updated 4.6 years ago • eb.mahmoudi

gt; Subject: [BioC] Expt. design question on optimal number of replicates > (in edgeR or else where) > > Hi Everyone, > Thanks to recent bioconductor workshop i atteneded ( and of course thanks > to Martin...for more powerful analysis. We have many RNAseq > libries with out replicates. And I read edgeR document and understand, not > much use …

RNASeq Organism edgeR RNASeq Organism edgeR

updated 12.3 years ago • Gordon Smyth

We are performing RNA-seq analysis in R using Rsubread and edgeR. We would like to be able to create a design matrix that allows our samples to be paired together. We have been following...We are performing RNA-seq analysis in R using Rsubread and edgeR. We would like to be able to create a design matrix that allows our samples to be paired together. We have been following the edgeR quasilikeli…

edgeR pairedsamples designmatrix

updated 3.6 years ago • sfidemw

<div class="preformatted">I would like to ask about design matrix in GLM model in edgeR. I have group of transgenic down regulate gene. We have 3 lines of transgnics per down regulate gene which different level...div class="preformatted">I would like to ask about design matrix in GLM model in edgeR. I have group of transgenic down regulate gene. We have 3 lines of transgnics per down reg…

edgeR edgeR

updated 12.0 years ago • Sermsawat Tunlaya-anukit

Greetings,     I have used edgeR to calculate fold-changes in gene expression between treated and untreated cells, each group consisting of three...Greetings,     I have used edgeR to calculate fold-changes in gene expression between treated and untreated cells, each group consisting of three replicates...estimate of error in fold-change for genes of our im…

edger rnaseq

updated 9.3 years ago • tstueve

Dear all, Both DESeq2 and edgeR normalization methods take into account different library sizes and RNA composition between samples, but are they

hemoglobin edgeR deseq2 normalization rnaseq

updated 5.6 years ago • aec

Dear all, I'm trying to apply edgeR to the analysis of a peptide screen and I have a few questions I hope I can get help with. __Background__ We are following...if nothing is misbehaving then when this data is analysed in an RNA-Seq type analysis framework like edgeR, we shouldn't see any differential enrichment between A30 vs NSP3 data. If we do then these are our "fast-growers". Note that...…

edger calcnormfactors peptide screen library size factor

updated 5.9 years ago • oakhamwolf

I have generated three DGE lists using the MakeContrasts function in EdgeR for pairwise comparisons of 3 conditions. I now want to make a union of these genes and cluster the expression (preferably

EdgeR clustering differential gene expression consensusclusterplus kmeans

updated 6.4 years ago • anupriya.dalmia

Hi, I can't seem to install edgeR due to an odd compilation error (see below). The error appears to be something about "make: \*\*\* \[R\_add\_prior\_count.o\] Error...Any ideas what might be missing (lib dependency)? Thanks, -todd   <pre> > biocLite("edgeR") BioC_mirror: https://bioconductor.org Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.1 (2017-06-30). I…

edger compilation error

updated 6.8 years ago • creasyt

isoforms of similar genes etc. which is not a problem for me - but will it effect the stats from edger as obviously some tags are counted multiple times. There are 40M tags in each experiment so I am assuming the aggregate

edgeR edgeR

updated 13.3 years ago • Dennis Gascoigne

than the knockdown samples, leaving us vulnerable to confounding batch effect. When I ran a standard edgeR pipeline (generalized linear model option, with pairwise contrasts between each knockdown model and the control...controls and all four knockdowns in the differentially-expressed genes. I put together a combined edgeR-SVA script to try and correct for the batch effect (shown below). I can c…

edger rna-seq sva differential expression

updated 7.4 years ago • mpj5142

Hi All,          I am analysing RNASeq data from human tissue samples for disease and normal patients. I have in  total 3 types of data: disease1 (n=12), disease2 (n=10) and normal (n=20). Some of my data were sequenced later and I see a clear batch effect. I am using EdgeR and design matrix is: design<-model.matrix(~SeqTag + …

edger FDR rnaseq

updated 7.2 years ago • dsarbashis

Hi, I am trying to use cqn offset in EdgeR and getting very low p-values (FDR < 10e-100). Is the offset working correctly?  Or I am missing some steps in the

CQN and edgeR

updated 6.1 years ago • Akula, Nirmala NIH/NIMH [C]

the OTU abundance table (this is, IMHO, the equivalent of the gene counts in RNA-Seq) and to use edgeR to perform an exact test or to do the equivalent analysis in Deseq2. When the comparison is made between samples which...sense methodologically? Please feel free to offer suggestions__. Question 2 (related): __Are Deseq2/edgeR suitable to test low diversity samples?__ I was told by someone wit…

edger deseq2

updated 9.0 years ago • Nick N

I am working on an RNA-seq dataset and have been using the EdgeR differential expression analysis methods with GLMs. Here, I have specified batch as a factor in the design matrix. The...I am working on an RNA-seq dataset and have been using the EdgeR differential expression analysis methods with GLMs. Here, I have specified batch as a factor in the design matrix. The batch factor is uncorrelated …

limma rna-seq removebatcheffect()

updated 6.7 years ago • Ekarl2

I am running a DE analysis on edgeR. I have 8 biological replicates, in groups of 2 (1 normal and 1 diseased) What I want to do is keep those genes, for which the

edger Tutorial

updated 6.1 years ago • ilovesuperheroes1993

I am new to limma-voom, so I apologize in advance for my ignorance. I am using limma to contrast the change in the transcriptome in response to a treatment between the sexes. I have paired samples. I filtered my data so that at least 2 libraries must have a count larger than a raw count of 5 in the smallest library. The following is the code I used: dge <- calcNormFactors(dge) \#for MDS …

limma limma voom edger

updated 7.6 years ago • gregory.l.stone

expression analysis, I have added this batch effect as an element in the design matrix in EdgeR and it works perfect. I also want to make a clustered heatmap from the genes that were found to be differentially expressed...the code I ran: <pre> # Loading required R libraries. library(gplots) library(limma) library(edgeR) # Define experimental factors and design matrix. batch &…

limma removeBatchEffect heatmap clustering

updated 8.7 years ago • Ekarl2

Dear EdgeR users I am working on a RNASeq dataset with extremely small sample size (2 samples in each group; N=4) and I am trying to find...Dear EdgeR users I am working on a RNASeq dataset with extremely small sample size (2 samples in each group; N=4) and I am trying to find any DEG's using these samples (I am aware of the consequences of using very small sample size). I did find some DEG's w…

edger pvalue sample size

updated 8.3 years ago • Venu Pullabhatla

So im trying to detect differentially abundant ASVs with the package edgeR, however when i get to this point i keep getting an error i don't understand: ``` counts <- as(otu_table(ASV_physeq.filt), "matrix...y = DGEList(counts=counts) y <- edgeR::calcNormFactors(y, method="TMM"); y <- estimateDisp(y, design); ``` Error: ``` Error in as.vector(x, mode) : cannot coerce ty…

edgeR edge

updated 21 months ago • Isa

Hello I'm having problem installing edgeR. it says gfortran lib is missing, wonder if anyone has a solution? Thanks! ```r clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names...1 (use -v to see invocation) make: *** [edgeR.so] Error 1 ERROR: compilation failed for package ‘edgeR’ * removing ‘/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/ed…

apple m1 installation silicon

updated 3.2 years ago • Brian

Hi there, I know it is a old question about the normalization of count using edgeR TMM methods.And I know using calcNormFactor(DEGList, method = "TMM") to get norm.factors.But how can I get the normalized...using raw count to divide the corresponding sizeFactors. So I wonder if there is similiar command in edgeR to directly output the normalized count matrix? And I have tried the cpm() functio…

edger normalization

updated 5.1 years ago • 15958021290

<div class="preformatted">Dear list, I am interested in adjusting for GC bias in my experiment. I have my data in an "SeqExpressionSet" object (using EDASeq library) called eset and I then run the following commands: dataOffset = withinLaneNormalization(eset,"gc", which="full",offset=TRUE) dataOffset2 = betweenLaneNormalization(dataOffset, which="full",offset=TRUE) y = DGEList(exprs(dataO…

Sequencing edgeR cqn EDASeq Sequencing edgeR cqn EDASeq

updated 11.5 years ago • Ying W

I am analyzing RNA-seq data using a hisat2 --> htseq-count --> edgeR pipeline. To do this, I am feeding CPM values generated by htseq-count into edgeR, which produces a "toptags" table, or list...don't seem to correlate to htseq-count's CPM values. For example, the toptags table generated by edgeR shows that for one gene there is a logFC increase of 0.73, however it doesn't look lik…

edger htseqcounts rnaseq

updated 7.8 years ago • romsdahl

From the results I see a general difference in logFC values for genes  from limma-voom, edgeR and DESeq2. Although some people saw difference in logFC between edgeR and EDSeq2 and got good answers (see[  here...https://support.bioconductor.org/p/75330/)), in my case edgeR and DESeq2 get very simmilar results but quite different from limma-voom. I found that (not sure, i saw it …

limma deseq2 edger rnaseq

updated 7.0 years ago • Jack