Bioconductor Forum

Hi, I ran diffbind and used edgeR and DESeq2. I have a question regarding the normalized counts. In the DESeq2 analysis, the normalized counts of one of...the samples always had integers. In EdgeR - there was no column with integers. In EdgeR normalization - one column is chosen as reference to all, and in DESeq2 they...create another column of the averages that is ussed for normalizatio…

diffbind normalized counts

updated 8.2 years ago • GFM

preformatted">Hi there, I'm writing to the list to have your comment about the possibility of using edgeR or DESeq for the analysis of ChIP-seq samples. Standard approaches to ChIP-seq analysis (relying on external software...going to test this anyway...). Since the negative binomial model stands for ChIP-seq analysis, both edgeR and DESeq should work well. One can use external software to ide…

edgeR DESeq edgeR DESeq

updated 11.9 years ago • Cittaro Davide

div class="preformatted">Dear the edgeR community, Good day. I'm analyzing my RNA-Seq experiment with edgeR. My study has 2 different genotypes (treeHS, treeLS) and

edgeR edgeR

updated 12.2 years ago • KJ Lim

div class="preformatted">Hi Mahnaz, Why don't you follow the advice of the edgeR User's Guide (as Mark has suggested)? All the case studies in the User's Guide describe how the filtering was done in a principled...used in the guide is a compromise of several considerations. BTW, there are newer versions of R and edgeR available than what you are using. Best wishes Gordon > Date: We…

edgeR edgeR

updated 10.4 years ago • Gordon Smyth

<div class="preformatted">Hi there Assuming you are talking about RNA-Seq data then differential expression analysis of exon expression can certainly be done using edgeR in the same fashion as if the counts were summarised at the gene level. The important thing is that you have raw counts for whatever features are of interest (whether genes, exons, methylation regions, etc.) as your input …

affy edgeR DESeq affy edgeR DESeq

updated 13.5 years ago • Davis McCarthy

I'm using `edgeR` to do differential expression analysis. In the output, there is this column `logFC`. I'm wondering how it was calculated...I'm using `edgeR` to do differential expression analysis. In the output, there is this column `logFC`. I'm wondering how it was calculated. Let's use one of my real cases for example. I have the expression of one gene from 6 treated samples and 6 control sa…

DifferentialExpression DEA FC FoldChange edgeR

updated 3.0 years ago • zhxiaokang

When i try to install the edgeR package i receive the error :   ld: warning: directory not found for option '-L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3...v to see invocation) make: \*\*\* \[edgeR.so\] Error 1 ERROR: compilation failed for package ‘edgeR’ \* removing ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/edgeR’ The downloaded source packages are...…

software error edger

updated 8.3 years ago • t3h096

div class="preformatted">Dear edgeR users and R community, I'm analysing a set of RNA-Seq data which has 2 different genotypes (treeHS, treeLS) and time of treatment...0H, 3H, 24H, 96H) with edgeR. After carried out estimating the common dispersion, the value of BCV for my RNA-Seq data was 0.428. > hl <- estimateGLMCommonDisp

edgeR edgeR

updated 12.1 years ago • KJ Lim

Hi, I am writing to clarify on the design matrix for running edgeR on data with multiple time points with two conditions. condition time Group sample1 condition1 T0 c1.to sample2 condition2...T1 c2.t1 sample5 condition1 T2 c1.t2 sample6 condition2 T2 c2.t2 Following section 3,3 in the edgeR manual, to find differentially expressed genes between condition1 and condition2 …

edgeR

updated 5.7 years ago • sharvari gujja

Bioconductor mailing > list <bioconductor at="" stat.math.ethz.ch=""> > Subject: [BioC] EdgeR glm based analysis > > Dear All, > > First, wish you all a very happy and prosporous New Year. > > In EdgeR manual[Case

edgeR edgeR

updated 10.7 years ago • Gordon Smyth

div class="preformatted"> Hi All, I am trying to use edgeR to find differentially expressed genes from a pairwise comparison. So I am following the edgeR's manual chapter 13: Case...X[,1] rownames(x)=geneid colnames(x)=colnames(X)[-(1:2)] group=factor(rep(c("N", "C"), 6)) # build edgeR object d = DGEList(x,group=group, genes=rownames(x)) # filter out genes have fewer than 1 count per milli…

edgeR edgeR

updated 12.9 years ago • Guest User

div class="preformatted">Dear Miguel, There is no assumption in edgeR that variances be equal between groups. The variance depends on the mean, and the mean depends on the library size, and...you're doing your own personalized analysis pipeline. I can only help posters using the standard edgeR pipelines. I may be understanding poorly, but your questions seem to be specific to your own data …

Regression edgeR DESeq Regression edgeR DESeq

updated 12.5 years ago • Gordon Smyth

adriaan.sticker at="" gmail.com=""> > To: bioconductor at r-project.org > Subject: [BioC] EdgeR GOF plots > > Dear all, > > I'm doing an EdgeR analysis and made some GOF plots after estimating > geneewise dispersion

edgeR edgeR

updated 10.6 years ago • Gordon Smyth

div class="preformatted">Dear edgeR community, Good day. I have sets of RNA-Seq data of 2 phenotype (HighS, LowS) plants with area TZ & SW (control). I used exactTest

edgeR edgeR

updated 11.5 years ago • KJ Lim

<div class="preformatted">Hello everyone! I'm using edgeR to detect DE genes on my data. I have 2 control samples and 4 mutated samples. I understand why I should filter them and I...div class="preformatted">Hello everyone! I'm using edgeR to detect DE genes on my data. I have 2 control samples and 4 mutated samples. I understand why I should filter them and

edgeR edgeR

updated 11.2 years ago • Catarina Almeida

Hi, I am willing to perform GSEA analysis on a sample set using the normalyzed counts from edgeR. However, I do not find a clear reference on how to obtain them. Would the line: cpm(y, normalized.lib.size=TRUE) (y being the...edgeR object already containing TMM normalization factors) be fine or other options are preferrable? Thanks, Luca

edgeR

updated 3.5 years ago • luca.s

<div class="preformatted">Hello everyone, I need to make a design matrix, and I can use the approach outlined in 3.3.1 of the edgeR users guide, but I think that there may be a better way to conduct the analysis. I have 36 samples in a 3x2x2 incomplete factorial...Hello everyone, I need to make a design matrix, and I can use the approach outlined in 3.3.1 of the edgeR users guide, but I th…

edgeR edgeR

updated 10.7 years ago • Sam McInturf

I would like to save the top genes that best distinguish the samples used to construct the MDS in edgeR but I don't know how. Is there a way to do it? Thanks in advance -- María Jesús García Pereira [[alternative HTML version deleted

edgeR edgeR

updated 10.6 years ago • María Jesús García

<div class="preformatted"> Dear Dr.Smyth, 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 Dr.Smyth, I am very interested in "Comparisons Both Between and Within Subjects" of edgeR. Because one of my study is according to this …

edgeR edgeR

updated 11.7 years ago • Guest User

<div class="preformatted"> Hi, All. Let me confirm my understandings about logFC and CPM of edgeR. 1."logFC" using glm functions are calculated from normalized factor. This process does not include transformation to...div class="preformatted"> Hi, All. Let me confirm my understandings about logFC and CPM of edgeR. 1."logFC" using glm functions are calculated from normalized factor. T…

PROcess edgeR PROcess edgeR

updated 10.4 years ago • Guest User

div class="preformatted">Hi, I got an below error message while running the edgeR. > d10 <- estimateTagwiseDisp(d10, prior.n = 10, grid.length = 500) Using grid search to estimate tagwise dispersion. &gt

edgeR edgeR

updated 13.3 years ago • Sridhara Gupta Kunjeti

wiki=""> On Mon, Aug 25, 2014 at 2:50 AM, assaf www <assafwww at="" gmail.com=""> wrote: > Dear Edger developers and users, > > I would like to compare transcription levels of orthologous genes belonging > to different...order to find significant species-dependent > changes in transcription levels. I though of using Edger for such > analysis. …

Transcription edgeR Transcription edgeR

updated 10.1 years ago • Tim Triche

I tried to normalize my data in edgeR as instructed in the respective vignette. I calculated _CalcNormFactors_ and then proceeded with estimating the

edgeR normalization calcnormfactors

updated 6.5 years ago • tkapell

Dear Bioconductor users, I am using the rpkm() function of edgeR and I was wondering how the rpkm value is calculated by this function. I tried: <pre> > library(edgeR) > rpkm function (x, ...) UseMethod...rpkm") <environment: namespace:edgeR></pre> So I tried: <pre> > UseMethod("rpkm") Error in UseMethod("rpkm") : 'UseMethod' used …

edgeR rpkm source code

updated 9.4 years ago • thibault.lorin

<div class="preformatted">Dear Jan, The first step is to read the documentation! Page 9 of the edgeR User's Guide says: "If the counts for different samples are stored in separate files, then the files have to be read separately and collated together. The edgeR function readDGE is provided to do this. Files need to contain two columns, one for the counts and one for a gene identifier. …

Normalization edgeR Normalization edgeR

updated 11.4 years ago • Gordon Smyth

<div class="preformatted">Hi, I am learning how to use edgeR to analyze RNA-seq data generated from Illumina GAII. The experimental design is fairly complex. I have a mixed 4x2 factorial randomized complete block design (RCBD) consisting of: 4 tissues: A, B, C, D 2 treatments: control, stressed 3 blocks: Block1, Block2, Block3 Tissue and treatment are fixed effects and block is a random…

edgeR edgeR

updated 12.6 years ago • Tilahun Abebe

library sizes based on the remaining counts, then scale normalize with calcNormFactors(). However, edgeR will be fairly robust against whether or not the rRNA genes are kept in or how much of the library they consume provided...gt; To: "bioconductor at r-project.org" <bioconductor at="" r-project.org=""> > Subject: [BioC] edgeR : Include or exclude structural/noncoding RNA > …

RNASeq edgeR RNASeq edgeR

updated 11.4 years ago • Gordon Smyth

<div class="preformatted"> Hi, I'd like to use a GLM in edgeR to adjust for a batch effect, though only one of my four batches has samples from both groups in the comparisons that I...div class="preformatted"> Hi, I'd like to use a GLM in edgeR to adjust for a batch effect, though only one of my four batches has samples from both groups in the comparisons that...1 2 3 4 pos 3 5 9 …

edgeR pvca edgeR pvca

updated 10.5 years ago • Guest User

Tophat/Bowtie => htseq-count => divide poly/rnp counts by input counts per gene/feature => edgeR differences between genotypes across polysome/rnp/input categories My question is thus: Is there a way to tell edgeR...to the input? Am I mucking things up my manually normalizing the read counts before giving them to edgeR? Thanks. Best, Scott Daniel Zarnescu Lab MCB Ph.D. Prog…

edgeR edgeR

updated 10.6 years ago • Scott Daniel

I was wonder if there is a specific way to incorporate relatedness into the design matrix for edgeR (or another tool for estimating differential expression)?&nbsp

edgeR related design matrix

updated 6.0 years ago • joanna.l.kelley

div class="preformatted">Hello, I am writing with a question about edgeR function smearPlot. I made a smear plot but am seeing rows of orange points below and above (-5,-5) and (5,5) respectively. Here

GO edgeR GO edgeR

updated 12.1 years ago • Ann Loraine

I imported a set of `salmon` quantifications into R with `tximport` default settings and exactly used the code on the manual page for [tximport][1] to prepare data for use with `edgeR`. The result is a `DGElist` with the offsets for the downstream DGE analysis. Issue: The `DGElist` (`y$samples`) does not contain the `lib.size` factors (they are all 1) for obtaining TMM-normalized counts via `c…

tximport edgeR

updated 4.7 years ago • ATpoint

div class="preformatted">Dear edgeR Users, Is there a possibility to extract the log likelihood values of genes under under GLM approach? Bests, Eszter -- Eszter

edgeR edgeR

updated 11.5 years ago • Ari Eszter

<div class="preformatted">Dear list, I posted a question few days ago with any success, so I decided to try again, explaining better my question and changing the header. I am analyzing RNA-Seq data with edgeR - DeSeq. I have two biological groups, two replicates each, and I want to test DE between the two biological groups. For instance, with edgeR, I calculated tagwise dispersion for ea…

edgeR DESeq edgeR DESeq

updated 12.5 years ago • Miguel Gallach

div class="preformatted">Hi, How does edgeR handle continuous variables? I would like to include variables like age and BMI in my analysis. As far as I have seen there

edgeR edgeR

updated 11.7 years ago • Fredrik Karlsson

div class="preformatted">We've made major performance improvements to the edgeR package. Changes made to the BioC devel ready for the next BioC release. The package now has a 50 page user guide with several...statistical issues have been solved, and even very large data sets are now handled in a few minutes. edgeR users might like to try out to new version. Best wishes Gordon </div

edgeR edgeR

updated 14.9 years ago • Gordon Smyth

Dear all, please could you let me know whether there is any major updates in the newest version of edgeR (for Bioconductor version: Release (2.13), http://www.bioconductor.org/packages/2.13/bioc/html/edgeR.html), as I am getting

updated 10.8 years ago • Bogdan

<div class="preformatted">Hello, I have used edgeR for DGE analysis and I have few questions regarding the model and comparisions. 1) What kind of statistical model is taken into account to analyze treatment structure and conduct analysis of variance? 2) How does the edgeR correct the multiple comparisions? 3) I am assuming that the calculated p-values in the output after performing the t…

edgeR edgeR

updated 13.3 years ago • Sridhara Gupta Kunjeti

Dear Bioconductor community, I'm currently exploring the implementation of edgeR for assessing differential abundance of metagenomics datasets. Briefly, I start with short Illumina reads, assemble...of up to a couple million genes (1 gene = 1 row) and 10s of samples (columns). I implemented the edgeR GLM methodology adjusting for block effects as suggested in the edgeR manual. Now my question c…

edger metagenomics gene abundance gene filtering

updated 8.9 years ago • jtremblay514

RNAseq data with limma::voom. In the [function documentation][1] it says > Note that [edgeR::voomLmFit][2] is now recommended over voom for sparse counts with a medium to high proportion of zeros. However, edgeR::voomLmFit...any downsides. [1]: https://rdrr.io/bioc/limma/man/voom.html [2]: https://rdrr.io/bioc/edgeR/man/voomLmFit.html [3]: https://www.bioconductor.org/pack…

edgeR limma voom RNASeq muscat

updated 9 months ago • annikagable

div class="preformatted">Hi all, I am currently using edgeR within a dog melanoma French project in order to find differentially expressed genes. One of the first steps of edgeR...methods base other attached packages: [1] edgeR_3.2.4 limma_3.16.8 > packageDescription('edgeR')$Maintainer [1] "Mark Robinson <mrobinson@wehi.edu.au>, Davis McCarthy\n<dmccarthy@wehi.edu.au>…

edgeR edgeR

updated 10.5 years ago • Mathieu Bahin

<div class="preformatted">There should not be a problem as long as you have read counts for each exon. The main issue is that you have little power if the number of reads for a feature is small. So you will need high coverage. You might want to use a normalization method such as the quantile method in edgeR, as I am not sure the others have been tested for this type of data. ( --Naomi …

Normalization edgeR DESeq Normalization edgeR DESeq

updated 13.5 years ago • Naomi Altman

<div class="preformatted">Dear list, I am a postdoc in Bioinformatics, working on gene/gene regulation using RNA-seq data. I would like to find the associations for a set of gene pairs that my collaborator sent me. I have 1000 such pairs whose counts are measured for 400 samples. One way to do it would be by simple correlations (Spearman CPMs) or by using limma (faster than edgeR and DESeq…

limma edgeR DESeq limma edgeR DESeq

updated 10.5 years ago • Panos Bolan

analyzing an RNASeq dataset, I have 3 samples with n=4 each. I was exploring the performance of both EdgeR and DeSeq and I noticed they vary a lot on the dispersion of the normalization factors. Using EdgeR calcNormFactors

RNASeq Normalization edgeR DESeq RNASeq Normalization edgeR DESeq

updated 11.5 years ago • Lucia Peixoto

html The short answer is to set the argument prior.n of the estimateTagwiseDisp() function in edgeR to a smaller value. The default in edgeR is to use a largish value for the prior df, which means that edgeR squeezes the tagwise...for your data. Try instead a smaller value like prior.n = 6/12. The smaller prior.n is, the more edgeR will de-prioritize those hyper variable genes. It would pref…

Sequencing edgeR DESeq Sequencing edgeR DESeq

updated 12.2 years ago • Gordon Smyth

div class="preformatted">Hi Everyone, I have been using edgeR for quite sometime. Most of our RNAseq data comes from infectious organisms like Malaria and Tryps. Our libraries generally...organisms/protocols). All these days, I have been ignoring them while doing the DE analysis using edgeR. I am NOT interested in differential expression of rRNA genes, but, worrying that excluding them from e…

RNASeq edgeR RNASeq edgeR

updated 11.4 years ago • gowtham

Hi All,  Thanks in advance for the help! I am still new to edgeR and welcome for any suggestions! I am trying to figure out which method is better off to analyze my data. I am interesting...Hi All,  Thanks in advance for the help! I am still new to edgeR and welcome for any suggestions! I am trying to figure out which method is better off to analyze my data. I am interesting…

edgeR limma offset

updated 6.4 years ago • catpaw.tw

div class="preformatted">Hello, I am new to this kind of analysis in MDS plot. I used edgeR for DGE analysis, which showed a great analysis of my results. I have one specific question regarding the MDS plot. For

edgeR edgeR

updated 13.5 years ago • Sridhara Gupta Kunjeti

we just want to see a ranked list of genes. I have used Cufflinks RPKM values, but if I want to use edgeR, is this a valid way of doing it using featureCounts: fc <- featureCounts(files=targets$Targets,nthreads=8, isGTFAnnotationFile...log=FALSE,gene.length=x$genes$Length) # Getting gene length from FeatureCounts, using rkpm() in the edgeR package, not Rsubread.. Then just write out thi…

RNASeq edgeR RNASeq edgeR

updated 10.4 years ago • Sindre

Hello! I'm an EdgeR user, and I would like to know how this program calculates the log2FC for 2 sets of samples (treated vs. control). For one...Hello! I'm an EdgeR user, and I would like to know how this program calculates the log2FC for 2 sets of samples (treated vs. control). For one gene...in control samples. But, if I do this operation manually, the result is not the same as the …

edger log2FC

updated 3.5 years ago • matteo.buti

thought I should summarize it for the original thread. After some investigation, it is clear that edgeR's problem with the TCGA RSEM "raw counts" is that they are not integers. edgeR is a likelihood- based package and it evaluates...then edgeR will run ok. I have made some changes to the edgeR GLM code on Bioc-devel so that it does this rounding automatically. (The...edgeR classic code was do…

RNASeq edgeR Rsubread RNASeq edgeR Rsubread

updated 10.6 years ago • Gordon Smyth

batch effects design <- model.matrix(~Batch+Batch:group) logFC <- predFC(y,design,prior.count=1,dispersion=0.05) I really appreciate it if someone can help me to get my design corrected and to get the batch

edgeR

updated 2.4 years ago • venura

a more sensitive detection of genes that are differentially expressed between conditions. However, EdgeR relies, precisely, on measuring biological variability to establish the statistical significance of differences...similar in the context of RNASeq and, more specifically, of the analysis of RNASeq data with EdgeR. Any comment will be more than welcome, as well as any relevant references. Th…

RNASeq Microarray edgeR RNASeq Microarray edgeR

updated 10.4 years ago • Guest User

div class="preformatted">Dear R and edgeR community, Good day. I have a question about parsing values from table. I have an R object, *ps*which contained a set of tags...which match to tags in the *ps* from a * DGEExact$table*. The DGEExact$table is generated with *edgeR* when performed the *exactTest* for the RNA-Seq data. The *DGEExact$table* is looks like: An object of class "DGEExact…

edgeR edgeR

updated 12.1 years ago • KJ Lim

Hi all, (edgeR Page no. 21,22 User Guide) I am running program of edgeR for without replicate . I am getting one one error so please help me...Hi all, (edgeR Page no. 21,22 User Guide) I am running program of edgeR for without replicate . I am getting one one error so please help me in that . ==================================== <pre> > bcv=0.2 > library(edgeR) &g…

edger without replicate

updated 8.8 years ago • Sushant Pawar

which is an offset matrix which can directly be used in a GLM type model (specifically edgeR). The usage is explained in the vignette secion on Import into edgeR. Previously the vignette recommended using the offset...in fact have the > multiplication by -1, but my eyes scanned over this: > > > library(edgeR) > > design <- model.mat…

GO edgeR cqn EDASeq GO edgeR cqn EDASeq

updated 11.5 years ago • Kasper Daniel Hansen

I had a question about using edgeR to perform inference on samples that have been sequenced and that have a consistent amount of external spike-in added...I would like to perform a differential expression analysis between the two treatment groups. edgeR inherently normalizes using TMM, treating the data as compositional. However, is it possible to use the spike-in information...of the spike-in. …

edgeR SpikeIn RNASeq

updated 3.5 years ago • robert.chen

div class="preformatted"> Hi, I am learning edgeR. I don't have any prior knowledge about programing language. When I got some exercises in case study 1, according to the...edgeR's user's guide, I got an error. > d <- readDGE(targets, skip=5, comment.char="!") Error in `colnames<-`(`*tmp*`, value = c("1", "2", "3", "4")) : length of

edgeR edgeR

updated 12.3 years ago • Guest User

Is it possible to have edgeR output contigwise variance? I'm looking to determine within and between group variance.&nbsp

edger

updated 7.8 years ago • nooria.alwathiqui

detailed analysis process of \"Comparisons Both > Between and Within Subjects\" of edgeR > > > Dear Dr.Smyth, > I am very interested in "Comparisons Both Between and Within Subjects" > of edgeR. Because one...gt; -- output of sessionInfo(): > > source("http://bioconductor.org/biocLite.R") > biocLite("edgeR") biocLite("li…

PROcess edgeR PROcess edgeR

updated 11.7 years ago • Gordon Smyth