Bioconductor Forum

Hi! I'm new to differential expression analysis and I don't understand quite well the edgeR's output. Maybe my questions will be basic knowledge but I will really appreciate any help. I've run a clustering analysis...would like to know the marker genes for each of the obtained clusters. So I'm doing pairwise DE with edgeR, that is, comparing each cluster against the others. My experimental des…

logFC edgeR DifferentialExpression scRNAseq

updated 3.1 years ago • mbenegas

div class="preformatted"> I am running edgeR on RNA-seq data with two groups Control(C1,C2,C3) and Treated(P1,P2,P3) having three replicates each. I need the log FC ratio...value in the numerator and Control(C1,C2,C3) in the denominator but the results I am getting with EdgeR are not well correlated with the read counts data that I have. e.g.: for gene Glyma12g14980.1 fold change (lg Fc) = 3…

edgeR edgeR

updated 12.9 years ago • Guest User

div class="preformatted">Hi I am still new to EdgeR and am using it to do pairwise comparisons of RNA seq data. I just realized that the sign of the fold change will be determined...I was looping through a list of comparisons and wondered why the sign changed. I am using v2.6.2 EdgeR. Thanks Bill [[alternative HTML version deleted]] </div

edgeR edgeR

updated 12.4 years ago • Spollen, William G.

Dear edgeR support team, In the tutorial its mentioned that Batch effects can be removed or corrected by using the additive model...formula. How can I visualise the removal of batch effect on the clustering of the samples using edgeR. <span style="line-height:1.6">Thanks and Regards,</span> Candida

edger batch effect

updated 9.7 years ago • candida.vaz

Is it possible to conduct a one-tailed differential expression analysis test using edgeR? I might have missed something in the documentation, but I cannot find anything definite. I mean by this conducting a...Is it possible to conduct a one-tailed differential expression analysis test using edgeR? I might have missed something in the documentation, but I cannot find anything definite. I mean by…

one-tailed edgeR DifferentialExpression test

updated 22 months ago • Sarah

<div class="preformatted">Hello, I am a graduate student and fairly new to RNA-Seq. In my study I have a 2x2 design with each group containing 4 bio reps and each bio rep has 3 technical replicates (same library prep, but each sample is processed in 3 different lanes). After studying my frequency count data I have found that the count data in lane 1 is very different from lane 2 and 3 for …

edgeR edgeR

updated 10.5 years ago • Neha Mehta

In edgeR, one usually estimates a common, trended and tag wise dispersion in order to estimate the mean-variance trend over all...In edgeR, one usually estimates a common, trended and tag wise dispersion in order to estimate the mean-variance trend over all genes. I have noisy data with large BCVs. It is actually single-cell RNA-seq, and just for comparison, I would like to analyse it with edgeR…

edger

updated 8.6 years ago • Koen Van den Berge

nbsp; Hi, I have problems installing edgeR on R-3.5.1. I get the following error at the end of the install: \*\* testing if installed package can be loaded Error: package...or namespace load failed for ‘edgeR’ in dyn.load(file, DLLpath = DLLpath, ...):  unable to load shared object '/opt/R-3.5.1/library/edgeR/libs/edgeR.so':   /opt...R-3.5.1/library/edgeR/libs/edgeR.…

edger install error

updated 5.9 years ago • jenny.russ

session and enter the commands: > source("http://www.bioconductor.org/biocLite.R") > biocLite("edgeR") > then edgeR version 2.2.5 will be installed on your system. I would recommend following the latest version of the edgeR...User's Guide, which was released with edgeR 2.2.x. You can get it from edgeR's Bioconductor page: > http://www.bioconductor.org/packages/2.8/bioc…

Epigenetics GO edgeR Epigenetics GO edgeR

updated 13.3 years ago • Davis McCarthy

div class="preformatted">Hi, I have done RNA-Seq using cuffdiff, edgeR, and Partek software And get a different list of differential expressed transcripts For all the software. Has anyone

edgeR edgeR

updated 12.9 years ago • Lana Schaffer

div class="preformatted">Dear list, I have a DGElist object in edgeR, already processed with calcNormFactors, estimateCommonDispersion and estimateTagWiseDispersion. Now, I would

edgeR edgeR

updated 10.5 years ago • Cittaro Davide

I am using edgeR to perform differential expression analysis. I have four different groups - three of them containing three samples...equal to NA? - At what points of analysis are p values set to NA? - What are the algorithms that edgeR uses to determine whether some gene will have p value = NA

DifferentialExpression edgeR

updated 14 months ago • miona.rankovic

Hi, I am trying to compare between 10 groups each with two replicates (RNA-seq data). I wish to determine the genes which distinguish each individual apart from one another. So far looking through the edgeR manual I have not found a way to compare all of the groups at once in order to obtain values such as logFC, logCPM, PValue, and FDR. Do you have any suggestions of how to compare all of these…

edger multiple comparisons anova glm

updated 9.3 years ago • chickenchamp4

Hi all experts, After doing DE analysis by edgeR, we can find the number of up and down-expressed genes by something like, "summary(de <- decideTestsDGE(lrt5))". I would &nbsp...me how we can export DE genes with all related information, like logFC, logCPM, P-value and FDR from edgeR software?  __3)__ As I found on net, we can convert cpm to rpkm via this f…

edgeR DE analysis fold change cpm

updated 8.1 years ago • Sara

I am a new R user trying to get up to speed on a genomics project and am attempting to install edgeR, but I am getting redirected to install BiocManager despite already having installed it. I have R 4.3.2 and BiocManager

edgeR

updated 8 months ago • quartet.trolls.0k

to environments, so all environments are equally represented among all batches. I lean towards EdgeR. I find it more user friendly and have used it more often, easier to select for a common-sense effect size in addition to...wants to use the mixed model approach of lme4 so that batch will be a random factor. Why does EdgeR not allow the use of random factors? What kind of arguments could I use i…

rna-seq edger mixed model random effects lme4

updated 8.2 years ago • Ekarl2

I would like to use edgeR to perform an ANOVA for difference between multiple groups, but am wondering what the best way is to do this. I have an...I would like to use edgeR to perform an ANOVA for difference between multiple groups, but am wondering what the best way is to do this. I have an RNA...I would like to use edgeR to perform an ANOVA for difference between multiple groups, but am wonder…

edger rnaseq anova

updated 7.5 years ago • Tony

<div class="preformatted">I have normalized my RNAseq read counts in EdgeR. If I try to look at the normalized data: total=cpm(w, normalized.lib.size=TRUE) And specifically the CPM values for my cell line 1 (in triplicates) for the gene Hspa5 total["Hspa5",1:3] 7492.944 6750.397 5727.190 If I find the fold change between cell line 1 and my control cell line 2 I get: total["Hspa5",1:3]/t…

RNASeq edgeR RNASeq edgeR

updated 11.1 years ago • CSRK (Christian Schrøder Kaas)

div class="preformatted">Hi guys, I would you to revise my edgeR code since it's possible I missed something important because being quite new on this. Thanks, Bernard P.S. This question...1067474 __ambiguous 0 __too_low_aQual 136484 __not_aligned 110488 __alignment_not_unique 0 ############################################################ #edgeR #########################################…

Alignment Organism topGO edgeR Alignment Organism topGO edgeR

updated 10.4 years ago • biotech

bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch=""> > Subject: [BioC] edgeR on microRNA data > > 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 that are not expressed at >…

microRNA edgeR miRNA

updated 3.3 years ago • Gordon Smyth

div class="preformatted">I try different contrasts with edgeR to get a feeling for my data and also to find out the best contrast for my question. I would like to know what genes are enriched

edgeR

updated 10.1 years ago • Guest User

Hi, I'm wondering if it could be possible to use "fitted values" from edgeR GLM model as normalized pseudo counts to be used as expression data matrix for further classification purpose. I implemented

edgeR GLM classification rnaseq

updated 8.6 years ago • Mattia

div class="preformatted">Hi all, when doing calcNormFactors using edgeR I obtain some NaN values. f=calcNormFactors(counts) V2 V3 V4 V5 V6 V7 V8 V9 1.0000000 0.9987462 NaN 0.7550607 0.6139919

edgeR edgeR

updated 13.6 years ago • Marina Naval Sanchez

Hi all, I'm a budding researcher learning edgeR primarily by reading through the official User's Guide. I'm analyzing an RNA-seq dataset with six samples, three in each...of two groups. I found the User's Guide a bit cryptic as to whether I should use the classic edgeR approach (exactTest) or the GLM functionality (glmQLFTest). I understand the classic approach is useful for experiments

factors edgeR setup DGELIst

updated 3.3 years ago • Alex

that enter into the statistical model. Such correction factors are usually computed internally by edgeR functions, but it is also possible for a user to supply them.I would like to supply the correct factor to edgeR, how could

Normalization edgeR Normalization edgeR

updated 10.6 years ago • Guest User

div class="preformatted">Der BioC edgeR developers and users: I am using edgeR for ncRNA transcriptome data analysis - ie mapping RNA seq results only versus

Normalization edgeR Normalization edgeR

updated 10.8 years ago • alessandro.guffanti@genomnia.com

<div class="preformatted"> I have a question about you edgeR, in order to fix a problem that may be very simple for you. I'm using `edgeR` to perform differential expression analysis from RNA-seq experiment. I have 6 samples of tumor cell, same tumor and same treatment: 3 patient with good prognosis and 3 patient with bad prognosis. I want to compare the gene expression among the two gr…

edgeR edgeR

updated 11.3 years ago • Guest User

Hi, If I want to test differential expression (DE) between treated and blank samples using edgeR, I need to perform a one-sided p-value test. This test will allow me to identify only the expressed sequences in the treated...samples. How can I perform a `one-sided test` for DE analysis in `edgeR`? Any help would be greatly appreciated

edgeR

updated 17 months ago • f_rahmdani

<div class="preformatted">Dear all, I'm doing analysis on allready mapped reads from sequencing data for differential expression with EdgeR. My experimental setup is as follow: I have samples from 4 different subjects. Material of each subject wast treated with 2 different treatments (and a control) for 2 timepoints. I want to analyse the effect of the treatments (compared to control and …

Sequencing edgeR Sequencing edgeR

updated 10.6 years ago • Adriaan Sticker

in my analysis results using the same data but two very close related methods: limma-voom and edgeR. for purpose of consolidation and comparison, since I try to get as accurate DEGs lists for my next step downstream analysis...for the same dataset, I used both edgeR and limma-voom originally try consolidate each other. Surprisingly, as shown below the numbers of DEGs for 4 constrasts...the resul…

RNASeq edgeR RNASeq edgeR

updated 10.6 years ago • Ming Yi

everybody, I am relatively new to R, so this might be a stupid question. I am actually working with edgeR and I'd like to extract a file with the normalized expression values. I do have the normalization factors in the DGEList

Normalization edgeR Normalization edgeR

updated 12.5 years ago • Philipp Brand

Hi guys! I want to know if edgeR also need to specify reference group data similar to DESeq2? Because DESeq2 need to use ``` dds$condition <- factor(dds...Hi guys! I want to know if edgeR also need to specify reference group data similar to DESeq2? Because DESeq2 need to use ``` dds$condition <- factor(dds$condition...to specify which group is reference group. But I didn't find…

edgeR reference group

updated 5.0 years ago • 15958021290

uniprot id's across three time points.I wish to perform differential gene expression analysis using edgeR. I checked https://www.bioconductor.org/packages/devel/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf and

differential gene expression edger

updated 6.2 years ago • prakashpandey1111

gt; > No, you have not understood me correctly. I did not suggest that you change > from edgeR to limma. I suggested that you read the limma documentation > because the design matrix is the same for edgeR as it is...vice versa" seems to be about absolute expression >>>>> levels. >>>>> edgeR doesn't test f…

limma edgeR limma edgeR

updated 12.1 years ago • KJ Lim

Dear all! I am analysing RNA sequencing data by using edgeR package, but I am not sure about how should I make the design matrix. The counts table are obtained by using Rsubread package...Dear all! I am analysing RNA sequencing data by using edgeR package, but I am not sure about how should I make the design matrix. The counts table are obtained by using Rsubread package. Firstly, I will descr…

bioconductor edgeR design and contrast matrix rnaseq differential gene expression

updated 8.1 years ago • lidixu.se

from DESeq2 would be "enough ? Or i could alternatively try the cpm transformation from edgeR, although they present some distinct characteristics ? 2) If i would like to use the cpm transformation, i should apply...For example: <pre> <span style="background-color:rgb(240, 240, 240)">logCPM.counts <- cpm(dt, prior.count=</span>2<span style="background-color:rgb(240,…

rnaseq analysis variancestabilizingtransformation normalization cpm edger

updated 6.4 years ago • svlachavas

Hello, I used the edgeR and DESeq2 to calculate the differentially expressed genes. Of course, the results are not identical. I read many papers

edger deseq2

updated 6.4 years ago • yueli7

div class="preformatted">Dear all, I'm trying to set up my analysis in EdgeR to look at differential expression at 4 time points (J, N, M, N) in three samples (A,B,C). Our hypothesis is that environmental...is the same for all genotypes setwd ("~/Desktop/CURRENT FILES/R Scripts/Bleaching_data") library(edgeR) # making a matrix of factors called "targets",Time=Time , SF = genotype targets &a…

Normalization edgeR Normalization edgeR

updated 11.5 years ago • Colleen Burge

Hello, Based on other threads on this forum, I was planning to use `` edgeR:::treatDGE() `` to select differential open chromatin peaks while taking into account fold change. I installed edgeR using...biocLite `` and `` library(edgeR) ``, and have been able to use many common functions from edgeR (i.e. `` DGEList ``, `` estimateGLM ``\*`` Disp ``, `` glmFit `` and `` glmLRT ``). However, R...ca…

edger installation

updated 9.6 years ago • ejliaw

nbsp;I have a problem about cpm filtering in edgeR. I have read the advice of the edgeR manual, where the typical filter is .. keep genes that have at least X samples with cpm

edger

updated 8.6 years ago • panagiotis.mokos

Dear all, I'm a newbie in edgeR and read multiple tutorials + the EdgeR manual but still did not figure out how to solve it. I'm running a DGE analysis with...animals, which is the reason why I'm trying to design a complex matrix (following page 42 from edgeR manual). I tried cbind tp and animal into a column in my lib_spec but it will not help when I run other sorts of comparisons

design model.matrix edgeR complexdesign

updated 6 weeks ago • Karla

batch effect between replicates collected on the same days. Then on the other hand, I tryed to use edgeR with TMM method to do the same, with and without adjusting for batch effect. And the thing is that I have really different...results. Ballgown always returns a lot of DEGs comparing with edgeR all of them with pval<0.05, but the most surprising thing is that if I compare ballgown and…

edger ballgown rnaseq batch effect adjustvars

updated 5.7 years ago • IRAIA.MAIALEN

Hi, I need to run an old version of edgeR 2.2.6. I found it on Bioconductor: https://bioc.ism.ac.jp/packages/2.8/bioc/html/edgeR.html The problem is that when...Hi, I need to run an old version of edgeR 2.2.6. I found it on Bioconductor: https://bioc.ism.ac.jp/packages/2.8/bioc/html/edgeR.html The problem is that when I...gt; setwd("/Users/Elena/Tnseq_ESSENTIALS_analysis_All_with_BG20h_runB…

edgeR

updated 7.7 years ago • elena.capel

<div class="preformatted">Hi Audra, Have you tried following the examples in Sections 4.1 and 4.2 of the edgeR User's Guide? However you will probably need to learn more about R itself to be comfortable, as Sam McInturf has noted in his reply. Best wishes Gordon > Date: Sat, 14 Dec 2013 18:51:08 -0800 (PST) > From: "Audra [guest]" <guest at="" bioconductor.org=""> &a…

edgeR edgeR

updated 10.8 years ago • Gordon Smyth

male and female) and I want to know which genes are DE between this two groups. Which approach of edgeR should I use? The classic one with exactTest function or the GLM approach. Thank you for your reply -- output of sessionInfo

edgeR edgeR

updated 11.9 years ago • Guest User

div class="preformatted">Dear edgeR users and developersï¼ I have few questions about edgeR when recently I use it for 454 pyrosequencing data: 1. prior.n

Normalization edgeR Normalization edgeR

updated 13.9 years ago • Ying Ye

Hi all, I'm a computational biologist at Children's Memorial Hospital in Chicago. I'm using the edgeR library to compare RNA-seq datasets. But, recently I was running a comparison and got an error that led me to the realization

edgeR edgeR

updated 12.4 years ago • Jared Bischof

<div class="preformatted">Hello, I have RNA-seq data from 10 normal samples and 8 tumor samples, which I am using edgeR to analyze for differential expression (DE) between the tumors and the normals. I have basically followed the workflow in the edgeR user's guide section 3.3. It is known that there is a large RNA compositional bias in these normal tissue samples (i.e. the...Hello, I ha…

Normalization edgeR Normalization edgeR

updated 12.2 years ago • Hoskins, Jason NIH/NCI [F]

div class="preformatted">Hi everybody, I just started using edgeR and DESeq and am looking for a confirmation that I am not doing a silly thing. Basically, we have 7 conditions and for only...Typically using the commands (note that I compare here "B" to "C", thus samples without replicates). edgeR: countTable=read.table('mytable',header=F,row.names=1) ; dge <- DGEList(counts=countTab…

edgeR DESeq edgeR DESeq

updated 11.8 years ago • Yvan Wenger

div class="preformatted">I've just starting exploring edgeR. Gotten an error I am unsure of... I'm following the how-to with no changes > d DGEList: $data lane3 lane8 lane5 lane6 1 0 0 1054

edgeR edgeR

updated 15.1 years ago • Paul Leo

Hi, I am a PhD student from Dept. Statistics of Penn State University. I have been using edgeR for my RNA-seq data recently. As I moved forward with edgeR, I found there are probably some bugs in the latest documentation

edgeR edgeR

updated 11.4 years ago • Guest User

clarify: I would like to plug in existing size factors into `vst` like `sizeFactors(dds) <- edgeR::calcNormFactors(count.matrix)` and then `vst(dds)` in order to use the exact same factors I used for DE testing with edgeR

DESeq2

updated 4.0 years ago • ATpoint

Dear List, I've been used edgeR for differential expression analysis for data generated from the same tissue, but different conditions. Now I have...generate RPKM value for my own data A. I already had a count table, and would like to use rpkm() in edgeR, but first I have to get a gene length vector. My question is how to count gene length from an "Ensembl.gtf" file by taking

RNASeq edgeR rpkm

updated 9.9 years ago • shirley zhang

offset=TRUE) offset <- offst(dataOffset)</pre> My goal is to incorporate “GC offset” into my edgeR pipeline  (not to override edgeR calculated offset). I found some suggestions online but I am not sure I am doing right

edgeR EDASeq offset

updated 6.7 years ago • alakatos

but if I then do: > > > source("http://www.bioconductor.org/biocLite.R") > > biocLite("edgeR") > > I get the error message: > > Using R version 2.14.0, biocinstall version 2.8.4. > Installing Bioconductor version...2.8 packages: > [1] "edgeR" > Please wait... > > Warning: unable to access index for r…

updated 12.8 years ago • David Fredman

want to calculate RPKM values of my data and, following previous posts, I use the function rpkm() of edgeR. Initially, I checked how the function works on the hypothetical data of http://blog.nextgenetics.net/?e=51 (__Measurement...webpage. Could someone please advice if there is actually a problem with the rpkm() function in edgeR? if yes, do I have to recalculate the values manually or is there…

edger rpkm

updated 9.6 years ago • Makis Motakis

Hi,     I am using edgeR for 65 pairs Tumor-Normal differential expression genes analysis. I want to get genes that differentially express...Hi,     I am using edgeR for 65 pairs Tumor-Normal differential expression genes analysis. I want to get genes that differentially express between Tumor samples and Normal samples. The methods I used ar…

edgeR

updated 9.5 years ago • zhouxiuqing

is ~300 samples x200.000 genes/count features). I have access to cluster computer. I want to use edgeR. Can I split this up into multiple run with batches of genes (i.e. run 20 runs with x 15,000 genes each), or will this distort

edgeR rnaseq

updated 8.8 years ago • martiningi

sssup.it=""> > To: bioconductor at r-project.org > Subject: Re: [BioC] How to design matrix on edgeR to study genotype x > environmental interaction > > Dear Gordon, > > Thank you so much for the reference. I read all...2012/10/30 Gordon K Smyth <smyth at="" wehi.edu.au=""> > >> Dear Daniela, >> &am…

Sequencing miRNA Normalization edgeR Sequencing miRNA Normalization edgeR

updated 11.8 years ago • Gordon Smyth

div class="preformatted">Hi, I am using edgeR for a 2x2 factorial design (Strain*Treatment) without any replicates and the estimateGLMCommonDisp and glmFit functions

edgeR edgeR

updated 13.2 years ago • Filippis, Ioannis