Bioconductor Forum

Hi, I am a master student in biomedicine at Lund University in Sweden. I am using edgeR for differential expression of genes. I am a beginner in the use of edgeR. ``` setwd("C:/Users/Analysis") library("edgeR") library...C:/Users/Analysis/Results/.../testedgeRtmmoutputN_par_1_73.csv") #To get logcpm logcpm <- cpm(y, prior.count=2, log=TRUE) write.csv(logcpm,file="C:/Users/Analysis/Resul…

RBioinf

updated 7 months ago • fr8712ca-s

gt;>> Subject: [BioC] Testing for differential expression variability with >>> edgeR >>> >>> Dear Bioconductor list, >>> >>> I am using edgeR to test for differential expression but I also...gt;>> R4.Cold and R5.Cold. Can I use the tagwise dispersion values p…

edgeR edgeR

updated 12.6 years ago • Gordon Smyth

In the past few releases, edgeR's glmLRT has supported an alternative significance test via the test="F" argument. However, I don't really see any documentation

edger dge differential expression

updated 9.3 years ago • Ryan C. Thompson

<div class="preformatted">Dear edgeR users, I worked my way through the user's guide of edgeR. However, I still have some questions and problems understanding the anova-like way of analyzing differential gene expression. I would be very grateful for any help or suggestion. I hope I did not overlook any earlier post concerning the same topic. My RNAseq data are derived from 4 different de…

RNASeq edgeR RNASeq edgeR

updated 11.2 years ago • Benedikt Drosse

div class="preformatted">I am using edgeR to analyze my RNA-seq data the data is paired-end and strand specific i have 6 sample 1-3 are biological replicate of one

edgeR edgeR

updated 12.6 years ago • wang peter

x 2 groups x 2 (pre & post)= 40 samples). Based on example from section 3.5 of the edgeR vignettes, I used the following the design in edgeR: <pre> ~ Treatment + Treatment:Patient + Treatment:Cond</pre> so my model

edgeR complex-design

updated 9.9 years ago • lwc628

<div class="preformatted">Hello Sir, I'm doing differential gene exp. by the edgeR package. My data seems to suitable to analyse by glm method (As per edgeR userguide section 3.5 Comparisons Both Between and Within Subjects). I have two different matrix to design. Matrix One: I have 12 dataset 3 samples from different healthy individuals (Healthy) of two different stages (npc,ne) and 3 sa…

edgeR edgeR

updated 10.5 years ago • Justin Jeyakani GIS

TPM , and FPKM values in a *.csv file for all samples (60000 genes * 18 samples). I understand `edgeR` can work with expected counts as output by `RSEM`, then normalize, and perform differential gene expression analysis...process since, I already have the batch corrected `TPM` and `FPKM` values, Is there a way in `edgeR` to import the TMP or FPKM values, and then only perform differential gene e…

DESeq2 R edgeR Normalization RNASeq

updated 22 months ago • mohammedtoufiq91

<div class="preformatted">Dear Assaf, You are getting the sort of results that I would expect you to get when you try to compare two RNA sources that are very different. The diagonal lines in the MA plot are simply a result of having low counts (0,1,2 etc) in one species and high counts in the other for the same genes. When you compare different species, I'd intuitively expect almost eve…

Normalization Organism edgeR

updated 10.0 years ago • Gordon Smyth

div class="preformatted">Hi there, I am analysing RNAseq counts using edgeR package. But I am running into problems because of 'zero' counts for certain tags in my data. The code syntax I am using is...not allowed if 'na.rm' is FALSE Could someone please suggest how to handle the missing values with edgeR normalisation methods ? Thank you Sonika ------------------- > sessionInfo() …

RNASeq edgeR RNASeq edgeR

updated 13.1 years ago • Sonika Tyagi

  In edgeR, given the following data table: GENE EXPRESSION DISEASE A B A1BG 3 1 0 0 A1BG 0 1 0 0 ... ZZZ3 6 0 0 1 ZZZ3 7 0 0 1 A: concentration of...nbsp; In edgeR, given the following data table: GENE EXPRESSION DISEASE A B A1BG 3 1 0 0 A1BG 0 1 0 0 ... …

limma edger rnaseq

updated 7.5 years ago • mousheng xu

<div class="preformatted">Hey Mark, A question on one-way ANOVA design with edgeR: I do something like that for 3 groups, so similar case like in the vignette (glm functionality): d <- calcNormFactors(d) d...div class="preformatted">Hey Mark, A question on one-way ANOVA design with edgeR: I do something like that for 3 groups, so similar case like in the vignette (glm functi…

edgeR edgeR

updated 11.3 years ago • Michal Okoniewski

Dear All, I would appreciate some help with writing a table out from a DGEExact object. I have used edgeR to produce an DGEExact output table. The data frame contains the log-concentration (i.e. expression level), the log- fold

Sequencing edgeR Sequencing edgeR

updated 13.8 years ago • Karen Sherwood

Hi, I have used Voom to transform my data with the TMM scaling factor and identified a list of differentially expressed genes for my RNA-seq data. What I want to do next, is to generate a bar plot on some genes of interest and also plot an expression heatmap. My question is, can I use the transformed E values from ```Voom``` for this, or should I recalculate the Log2CPM values using the ```cp…

edgeR limma

updated 12 months ago • petertam1343

I am so new in Bioinformatics, using R and edgeR. I used the following code: ``` targets <- read.delim("cell_line_M.txt", stringsAsFactors = FALSE) d <- readDGE(targets) colnames

logCPM edgeR

updated 3.6 years ago • H

of dispersion for the expression of each gene, and GLM is preferred compared to the classic edgeR approach for >=2 factor design which is why I have chosen the use of these 2 functions in my R script for EdgeR DGE analysis

edgeR

updated 2.5 years ago • melatoninixo

workflows (RNASeqGeneEdgeRQL and rnaseqgene which rely on edgeR quasi-likelihood and DESEQ2 respectively). I obtained different results I'm quite perplexed about, both in terms of...in higher expression levels for different transcripts, and with the following parameters: For edgeR fc <- featureCounts(all.bam, annot.ext="pathofmygff3", isGTFAnnotationFile=TRUE, nthreads=16, GTF.fe…

edger deseq2 rnaseq de

updated 4.4 years ago • Raito92

Hello everybody, I have analysed an experiment of ribodepleted samples using both DESeq2 and edgeR robust. I read that one can expect a concordance of 70-80% between both tools. Here, this is not the case. In this experiment...Hello everybody, I have analysed an experiment of ribodepleted samples using both DESeq2 and edgeR robust. I read that one can expect a concordance of 70-80% between bot…

deseq2 edgeR differential gene expression

updated 8.3 years ago • Jane Merlevede

I am trying to conduct edgeR and Iam facing with 'Warning message: In estimateDisp.default(y = y$counts, design = design, group = group, : No residual df: setting...ABCDEFGHIJKLMNOPRSTU4.txt" ) read.delim(files[1]) library(limma) library(edgeR) x <- readDGE(files, columns=c(1,3)) class(x) dim(x) samplenames <- substring(colnames(x), 12, nchar(colnames(x))) samplena…

edger

updated 5.1 years ago • trumbia

It is considered best practice to use the calcNormFactors function in edgeR or rely on voom for normalization across samples? Using `calcNormFactors`: voom(calcNormFactors(DGEList(counts)), design

edgeR limma

updated 3.2 years ago • P1000

for any input. Daniela 2012/10/30 Gordon K Smyth <smyth@wehi.edu.au> > Dear Daniela, > > edgeR can work with any design matrix. Just setup your interaction model > using standard R model formula. See for example...sssup.it> >> To: bioconductor@r-project.org >> Subject: [BioC] How to design matrix on edgeR to study genotype x &a…

Sequencing miRNA edgeR Sequencing miRNA edgeR

updated 11.9 years ago • Danie

I have some question about normalization in package tweeDEseq which using TMM method in edgeR to normalize count data. I run normalization as manual and found something unusual. The read count before normalization...header=T ) > group <- c(1,1,1,2,2,2,2,3,3,3,4,4) > yN <- normalizeCounts(y, group) Using edgeR normalization methods. Calculating library sizes from column…

Normalization edgeR tweeDEseq Normalization edgeR tweeDEseq

updated 12.6 years ago • Sermsawat Tunlaya-anukit

div class="preformatted">Dear Mike, edgeR uses the term 'offset' in the same way that has been standard for generalized linear models since Nelder and Wedderburn...20 10:11:45 CET 2013 Michael Love love at molgen.mpg.de [BioC] using offsets from EDASeq and cqn for edgeR But I think it would be desirable for packages on both sides of the hand-off to provide an explicit formula for what is

cqn EDASeq cqn EDASeq

updated 11.6 years ago • Gordon Smyth

I used the tximport pipeline upstream quantification methods (Salmon) in order to further use EdgeR pipeline. I am confused about normalization part. As in the (https://bioconductor.org/packages/release/bioc/vignettes...I used the tximport pipeline upstream quantification methods (Salmon) in order to further use EdgeR pipeline. I am confused about normalization part. As in the (https://bioconduct…

edger normalization

updated 4.1 years ago • ahmedaalkarim

div class="preformatted"> Dear list, when using edgeR GLM after running estimateGLMCommonDisp I am getting this error: Error in solve.default(R, t(beta)) : system is computationally

edgeR edgeR

updated 11.9 years ago • Guest User

The reference for DESeq2's estimateDispersions() says that it uses Cox-Reid likelihood that was originally implemented in edgeR in 2010. I take it (correct me if I am wrong) that one drawback of CR vs GLM is that GLM can incorporate the effective library size as an offset, whereas CR can't. For that reason, counts have to be normalized prior to applying CR. In DESeq2 normalized counts are obtain…

deseq deseq2 edgeR normalization

updated 8.8 years ago • Nik Tuzov

<div class="preformatted">Dear Sindre, Just run edgeR as usual on all genes. Run topTags() with n=Inf to get a table of DE results for all genes: tab <- topTags(yourresults, n=Inf) Then...div class="preformatted">Dear Sindre, Just run edgeR as usual on all genes. Run topTags() with n=Inf to get a table of DE results for all genes: tab <- topTags(yourresults, n=…

edgeR edgeR

updated 10.6 years ago • Gordon Smyth

<div class="preformatted">Hello Bioconductors, For some data, the code below works great and I find differentially expressed genes. However, I have added some biological replicates to the data, which caused warnings and then an error. The warnings come from the estimateGLMTagwiseDisp function, then an error appears in the glmLRT function. I tried the development version of R and edgeR bu…

edgeR edgeR

updated 11.9 years ago • john herbert

div class="preformatted">hi, in both edgeR and DESeq2, estimation of dispersion precedes negative binomial GLM fitting. my question is, can I use a design formula

edgeR DESeq2 edgeR DESeq2

updated 10.3 years ago • Iddo Ben-dov

div class="preformatted"> Hello, I am using EdgeR to analyse my RNAseq data. I have: cells from 3 healthy patients , either treated or not with a hormone . cells from 3 patients

RNASeq edgeR RNASeq edgeR

updated 11.9 years ago • Guest User

I have rna-seq data (18 samples) from which I produced the raw counts using htseq-count. Now I want to analyze the data using edgeR. I've done this dozens of times and had no issues. Not this time. When I execute <pre> samples <- read.csv(file="metadata_composite.csv",header=TRUE,sep=",") counts <- readDGE(samples$CountFiles)$counts </pre> I get: <pre> Error…

edger rna-seq

updated 9.2 years ago • Nick N

Hello, I'd like to run edgeR on a MeDIP-Seq experiment with 4 treatment groups (each with 5 samples). I'm counting reads in slides over the genome (a few...I subtract the normalised input from my IP per window when the downstream analysis is done with edgeR or would this violate the statistical assumptions or interfere with edgeR's internal normalisation of the data? &nbsp

edge

updated 8.9 years ago • Arne Muller

div class="preformatted">Hello, I was using edgeR to do differential expression on a RNA-seq dataset, but when I check the p.value (not adjusted) distribution of the output

edgeR edgeR

updated 12.7 years ago • Yuan Tian

Hi I was analysing public RNA-Seq datasets from GEO for arriving at the most affected pathways /GO terms using the edgeR program. My objective was to determine whether Ca signalling pathway had a considerable effect in the corresponding phenotype. I did a DE analysis with edgeR and arrived at result in which the Ca signalling pathway was one among the top (topKEGG) hundred pathways : (No.80) &a…

rnaseq differential expression edgeR kegg

updated 6.5 years ago • fawazfebin

Hi wondering why with identical settings other than EdgeR vs DeSeq2 would I get 5 orders of magnitude more diff peaks with EdgeR? Thanks

diffbind

updated 7.7 years ago • rbronste

RNA-Seq data from human tissue and want to compare the gene expression in cases and controls using EdgeR. If I want to adjust for the confounding effect of RIN, age and PMI; what is the correct way to do this? Here is my code: ``` library...edgeR) x <- read.delim("rawCountMatrix.txt", row.names = "Gene") group <- factor(c(1,2,2,2,2,2,1,1,1,1)) RIN <- c(5.6,7.6,6.7,5.6…

edger confounding

updated 5.3 years ago • Victoria

be placed in the appropriate slot on the DESeqDataSet for the full count matrix." However, with edgeR, the process is possibly not as straightforward; DESeq has a sizeFactor slot in the CountDataSet object, whilst...edgeR has lib.size and norm.factors slots in a DGEList object. lib size and size factor are different things...the assumption that norm.f…

edger ercc

updated 9.8 years ago • John

no treatment), (antibody of interest, control Ig antibody)? I believe that one could do this with edgeR utilizing count data from chipseq and creating a DGEList with the group representing each individual chipseq run...matrix to calculate norm factors, estimate dispersion, and perform glmQLFtests (following p.8 of the edgeR manual

diffbind edger

updated 6.6 years ago • james.dalgleish

This post is in response to a number of emails and posts asking about reading data into edgeR and producing RPKM. #Reading a data file containing both counts and annotation Suppose we start with a tab-delimited...ae23218c) The file contains counts but also gene IDs and an annotation column. To read this into edgeR: ``` library(edgeR) Data <- read.delim("counts.txt", sep="\t", row.names=…

rpkm edgeR featureCounts

updated 12 months ago • Gordon Smyth

Hello everyone I am using edgeR for the analysis of allele-specific expression events with mouse RNA-Seq dataset. <span style="line-height:1.6">I...Hello everyone I am using edgeR for the analysis of allele-specific expression events with mouse RNA-Seq dataset. <span style="line-height:1.6">I use...to both (i.e. Reads that don't overlap a SNP). Then I</span>&…

edger

updated 9.4 years ago • Vivek.b

div class="preformatted"> Hi Gordon, I have one more question about edgeR. I have used different normalization methods to normalize the data and then test the main effects, the two-way interaction

edgeR edgeR

updated 10.6 years ago • Guest User

Hello, I am working on edgeR version 3.2.3. From the documentation, I guess the "plotMDS.DGEList" is similar to PCA. The manual mentions that...Hello, I am working on edgeR version 3.2.3. From the documentation, I guess the "plotMDS.DGEList" is similar to PCA. The manual mentions that "Distances

edgeR

updated 9.5 years ago • Manoj Hariharan

to proceed with the GO analyses. How can I get a list of the up and down regulated genes from the edgeR? Best regards, Rodrigo

GOanalyses edgeR DEgeneslist

updated 3.6 years ago • Rodrigo

is there a recommendation and I hear someone said limma will give more false positive compared to edger and deseq2, is that true? here is the detailed code of trend and voom If the sequencing depth is reasonably consistent...than about 3-fold. In the limma-trend approach, the counts are converted to logCPM values using edgeR's cpm function: > logCPM <- cpm(dge, log=T…

limma

updated 4.1 years ago • linouhao

Hi all, I'm starting to use the tximport package to pull in salmon output for statistical analysis and I just wanted to verify that it is fine to use the non-integer counts with edgeR and DESeq2. Years ago, we needed to round the decimal counts from e.g., cuffdiff, but the tximport vignette implied the non...statistical analysis and I just wanted to verify that it is fine to use the non-integer …

tximport edgeR DESeq2

updated 7.9 years ago • Jenny Drnevich

Dear all, I do have a statistical question about the use of limma /edgeR/ DEseq2 in order to assess the differential binding / differential peaks in condition1 versus condition2. I only have...Dear all, I do have a statistical question about the use of limma /edgeR/ DEseq2 in order to assess the differential binding / differential peaks in condition1 versus condition2. I only have bigwig …

DESeq2 edgeR

updated 23 months ago • Bogdan

between groups 1 and 2 (call this {1⋂2}). Is this possible? The vignettes for DESeq2 and edgeR seem to only describe how to obtain regions that differ between groups. **Second,** assuming I now have {1⋂2}, I next need to obtain...genomic regions in groups 3 and 4 (call this {3⋃4}). I think I could do this in a similar fashion to edgeR's example, ((drug.2hr - drug.0hr) - (placebo.2hr - placebo.…

deseq2 design formula design matrix edgeR ATAC

updated 4.8 years ago • corinne_hutfilz

Hi everyone, we normally use EdgeR to analyze sequencing data from genetic screens (i.e. the data is the abundance of a reagent like a barcode or a gRNA under...considerably). However, I am not sure what type of tool to use for the next step: what kind of EdgeR-like approach would work for ranks? Thanks so much for any thoughts. KN

EdgeR rank

updated 8.3 years ago • knaxerova

if it is possible to extract gene-wise variance covariance matrices of the GLM coefficients in edgeR. I would like to use it for non-standard multiple comparison procedures. Thank you. &nbsp

edger

updated 8.1 years ago • Koen Van den Berge

Hi everyone, I’m following section 4.7 in the using EdgeR user guide for differential methylation analysis using the count data associated with GSE86297 from GEO. My output...lt;- -Out$distance[Out$neg] : NAs are not allowed in subscripted assignments ``` I installed EdgeR today using install("edgeR") and my session info is below. I’ve exhausted Google trying to figure this out…

edgeR nearestTSS

updated 4.6 years ago • amlivernois

<div class="preformatted">Hi Mark, This is an analysis question rather than a devel suggestion, so I've transferred it from Bioc-sig-seq to Bioconductor. Hope you don't mind. If you have divided your samples into two groups, and you have 7 samples, then I recommend you set prior.n=4. See https://stat.ethz.ch/pipermail/bioc-sig- sequencing/2011-June/002042.html for an explanation. I c…

edgeR edgeR

updated 13.3 years ago • Gordon Smyth

div class="preformatted">Dear Uli, edgeR is probably the fastest of the glm negative binomial packages, as we have done a lot of work moving all the fitting code...fit <- eBayes(fit) topTable(fit, coef=5) and so on. Alternatively, you would stick to edgeR and use the quasi-likelihood pipeline: y <- DGEList(counts = reads) y <- calcNormFactors(y) y <-…

edgeR edgeR

updated 10.3 years ago • Gordon Smyth

methylation frequencies due to biological and technical factors. I basically followed the steps in edgeR tutorial and the f1000 paper, however the results (particularly the logFC) look weird. Here is what I did: 1 load files ``` yall...Max. # Inf Inf Inf Inf Inf Inf fit1 <- glmQLFit(y, design, robust=TRUE, prior.count=2) ``` file.df is like ``` head(file.df,1) …

edgeR MethylationArray

updated 6 months ago • mico

by the vst method), can I extract an equivalent table (with the transformed values) using the edgeR method? The edgeR manual allows you to extract the normalised table converted to logCPM but this is not the negative

DESeq2 edgeR RNASeq DifferentialExpression

updated 16 months ago • Sofía

Hi, I have done differential expression on same date with both of DESeq2 and EdgeR but I am seeing contradict results. For instance DCK6 shows positive 1 fold change by DESeq2 while -1 fold change by EdgeR...0.4473959 S100A7A 351.9248 1.049479 0.3290714 3.189213 0.0014266070 0.1329832 For EdgeR > group = condition > group [1] TRG1-2 TRG1-2 TRG1-…

desEQ2 edger

updated 5.7 years ago • Fereshteh

Normal1 Normal2 Tumor1 Tumor2 when setting up the list of samples for differential analysis in edgeR, group <- factor(c("normal","normal","tumor", "tumor")) y <- DGEList(counts=x,group=group) y <- calcNormFactors(y) y <- estimateCommonDisp

edger

updated 8.3 years ago • Bogdan

The edgeR vignette talks about additive models when dealing with paired samples (and then also when adjusting for batch effects

edgeR

updated 3.8 years ago • science555111

<div class="preformatted">Hello, I am working with count table that has very big lib.size: > dge at .Data[[2]]$lib.size [1] 3.2e+08 4.2e+08 4.5e+08 3.8e+08 2.3e+08 2.1e+08 3.3e+08 2.8e+08 This causes CPM very small, and consequently very negative logCPM. This is 'head' of my cpm(counts): C1 C2 C3 C4 T1 T2 T3 T4 00000001 0.000 0.0000 0.0000 0.0…

updated 10.1 years ago • Vang Le

div class="preformatted">Hi, I've time course RNA-seq data that i would like to analyze using edgeR : Q1) shall i normalize using calcNormFactors() or glmFit() and glmLRT() do this normalization ,therefore no need to use calcNormFactors

Normalization Normalization

updated 12.9 years ago • Asma rabe

Hi, I would like to know if the order of the covariates when constructing the design matrix for edgeR software matters. For example: design = model.matrix (~0+sex+batch+condition) is the same as : design = model.matrix (~0+condition

edger differential expression covariate batch effect glm

updated 8.7 years ago • aec