Bioconductor Forum

Dear Bogdan, The advice in the edgeR User's Guide about using `estimateGLMCommonDisp()` with `method="deviance"`, `robust="TRUE"`, `subset=NULL` is intended to be used...at="" imls.uzh.ch=""> > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] edgeR > > Hi Mark, > > I have two samples "Y" and "S" (with no replicates), and following edgeR &am…

edgeR

updated 2.3 years ago • Gordon Smyth

significance meauses something slightly different.) The predFC() and glmFit() functions of the edgeR package have offered "predictive fold changes" for quite a few years, and they would still be my choice for this purpose...voom and DESeq2 are more recent alternatives, but I still recommend predFC() with prior.count=3 or 5 for this purpose. And predFC() will work even without biological replica…

limma edgeR limma edgeR

updated 10.7 years ago • Gordon Smyth

become equal to each other as the sample size goes to infinity.</span> <span style="line-height:1.6">edgeR has a similar problem. I fitted Negative Binomial regression separately for each gene, and the results are consistent...with edgeR output for a large sample. However, edgeR\_Robust stands apart, just like voom.</span> <span style="line-height:1.6">I find this

limma edgeR

updated 8.9 years ago • Nik Tuzov

but I am new to bulkRNAseq and would like to analyze paired FastQ files with DESeq2, rnaseqGene, or edgeR. Could anyone provide me with some simple code to get started? I would be happy to use any of the packaes. It seems like the

DESeq2 edgeR rnaseqGene

updated 20 months ago • vpl685

Hello, Thanks for the awesome tool. We are using edgeR for the RRBS for differential methylation analysis on multi regional tumors (multiple regions collected from each...library for regionA and one library for regionB in a tumour) I see you have some suggestions to run EdgeR when there is no replicate but I am wondering how it should be performed for the methylation data, not gene expression

RRBSdata edgeR

updated 8 months ago • annasoudi

counts created by `withinLaneNormalization()` and put it in DESeq2 pipeline, the same I did in edgeR. While, the user's guide suggest that both DESeq2 and edgeR expect un-normalized counts, if user need EDASeq or cqn normalization...using EDASeq+DESeq2 or edgeR, like https://support.bioconductor.org/p/108765/ and https://support.bioconductor.org/p/113405/ , both of them use "offset...method i…

deseq2 normalization RUVg edger

updated 5.1 years ago • Yang WY

When I conducted a differential gene expression analysis by using edgeR, I ran into a weird result. I performed the following commands. ```r > library( edgeR ) > library( dplyr ) > a01 <- read.table

edgeR

updated 1 day ago • hiroko.ohmiya

of dispersion computed using other packages or other methods in replacement of that computed by EdgeR.  The reason why I asked is I still want to use the GLM machinery of edgeR, but wanted to use the custom computed dispersion

edger

updated 9.6 years ago • lwc628

Hello, I'm attempting to run a glm analysis with edgeR on 32 biologically independent samples, with 3 factors. I have sex, age, and genotype. I'd like to create a full design matrix...timep12" "sexm:genoKO:timep2" [16] "sexm:genoKO:timep6" </pre> From what I understand of the EdgeR manual, the first 6 fields of the design matrix are the coefficients of each factor, against the baseline o…

edger glm rnaseq

updated 6.8 years ago • Denniswu

div class="preformatted"> Hi, I am using the package edgeR to determine differentially expressed genes in RNA-seq data. I have 8 samples, corresponding to 3 patients (2 conditions...0.00014959" "0.03479503" "0.03522840" "1.84247667" Since I was not able to find the details used in edgeR to calculate the model easily, I was wondering if from this glm-fitted values is it reasonable to obtain su…

edgeR edgeR

updated 12.8 years ago • Guest User

div class="preformatted">Dear All: I am using edgeR for RNA-Seq data analysis. According to the paper "Differential expression analysis of multifactor RNA-Seq experiments

edgeR edgeR

updated 11.4 years ago • Gu Mi

Greetings, I have an RNA Seq experiment looking at the impact of a stressor on several fish species. The analysis in edgeR went smoothly in all but one species where I could only identify a few deferentially expressed genes. This fish has been...an RNA Seq experiment looking at the impact of a stressor on several fish species. The analysis in edgeR went smoothly in all but one species where I co…

edgeR p-value distribution

updated 6.2 years ago • approximately.random

add gene counts for technical replicates)?  2. How should the design matrix be setup in edgeR

edgeR rna-seq replicates

updated 9.6 years ago • eb0906

an MDS Plot to check if my normal and diseased samples are being clustered well. I am running edgeR for the analysis. Could anyone tell me the difference between the 2 methods given below? I have inputted my file of raw

edgeR plotmds differential gene expression MDS mdsplot

updated 5.7 years ago • ilovesuperheroes1993

Hi everybody, afer reading some posts about different DE analysis provided by edgeR, I found that the QL framework it's a the better choice, as it provides more accurate type I error rate control. However...Hi everybody, afer reading some posts about different DE analysis provided by edgeR, I found that the QL framework it's a the better choice, as it provides more accurate type I error ra…

edgeR DifferentialExpression

updated 3.4 years ago • Marianna

such a batch effect, could you please kindly tell me how I can include this batch effect in edgeR analysis? Thank you in advance

batch effect edgeR RNA-seq

updated 5.6 years ago • Sara

two tissues (brain/heart) with two level of infection (infection vs no infection) and I am using edgeR to detect differential expressed genes between the tissue according to the infection status. I am hesitating between

edgeR RNASeq DifferentialRegulation

updated 17 months ago • bioinfoWanderer

Hi All, I have noticed a discrepancy when identifying differential binding sites using either edgeR or DeSeq2. I do not believe this is a normalization issue as I have checked both the box and MA plots using both raw and...Hi All, I have noticed a discrepancy when identifying differential binding sites using either edgeR or DeSeq2. I do not believe this is a normalization issue as I have checke…

diffbind

updated 7.8 years ago • cnova1950

div class="preformatted">Hi, I recently upgraded edgeR from 3.0.8 to 3.2.3 and I'm noticing some differences. I have some data that I normalized with EDASeq. I attempted to calculate

edgeR EDASeq edgeR EDASeq

updated 11.3 years ago • suzy.stiegelmeyer@syngenta.com

Hi, For few of my plant samples with no biological replicates I am using edgeR. If I use bcvvalue 0.1, I am getting >10k significantly differential expressed transcripts out of 47310 transcripts...Hi, For few of my plant samples with no biological replicates I am using edgeR. If I use bcvvalue 0.1, I am getting >10k significantly differential expressed transcripts out of 47310 t…

edger

updated 7.6 years ago • manoharankumar01

style="line-height:1.6">Hi all, How would you use the ballgown package in conjunction with voom, edgeR, DESeq, limma?</span> <span style="line-height:1.6">The bioarXiv paper seems to be making the claim that ballgown gaps the bridge...between cufflinks and tools like Limma, Voom, edgeR, DEseq.  </span> <span style="line-height:1.6">I don’t understand…

limma rnaseq differential expression voom

updated 9.7 years ago • François Lefebvre

Hi Gordon Smyth and other authors of edgeR, It seemed that the colnames of design2 on page 34 in edgeR User's Guide were wrong. They should be (intercept), groupA and

edger

updated 5.1 years ago • 2002ymx02

I have recently obtained very promising results using the diffSplice and diffsSpliceDGE from limma/edgeR, respectively. I was surprised to find that neither method has a cited reference despite being included in both the...I have recently obtained very promising results using the diffSplice and diffsSpliceDGE from limma/edgeR, respectively. I was surprised to find that neither method has a cited …

edgeR limma diffSplice DEXSeq

updated 8.1 years ago • maltethodberg

Hello, I am working on an RNAseq project in EdgeR and I have a random effect variable that I am not sure how to best deal with since EdgeR doesn't use mixed models. I have three...main questions: 1) how have people dealt with random effects in EdgeR, or do you use different programs to accomplish this? 2) How are blocking and batch effects different in EdgeR (the manual...from the S2h mesocosm a…

edger rnaseq

updated 4.8 years ago • emb13

https://en.wikipedia.org/wiki/MA_plot), it is normalized with LOESS. I was not able to find if edgeR performs something like loess normalization for log2Fold changes as it seems that the values are always centered

deseq2 edger

updated 8.7 years ago • tonja.r

The help page for `edgeR::calcNormFactors()` says > The default method was changed from "TMM" to "TMMwsp" in the Bioconductor 3.9 release. However

edger

updated 5.1 years ago • Homer

Dear all, i'm doing a DEGs analysis on edgeR.  Count reads are from a RNA-seq experiment based on 2 thesis and 3 bio. rep.s each. We're talking about 10k genes odd...Dear all, i'm doing a DEGs analysis on edgeR.  Count reads are from a RNA-seq experiment based on 2 thesis and 3 bio. rep.s each. We're talking about 10k genes odd. (so

edgeR DEGS common disperion

updated 7.1 years ago • baus87

Hi, Time to tackle an amateur's problem! Ha ha! I have 6 samples/ groups with 3 replicates (In total 17; one sample contains 2 replicates). the sample names are Mf, Bf, Ef, Mr, Br, and Er. I want to get DEGs (differentially expressed genes) between Mr-Mf, Br-Bf, Er-Ef. For doing that, I subsetted my data keeping either Mr-Mf, Br-Bf, or Er-Ef. And then I got DEGs for three different contra…

subsettingdata edgeR designmatrix

updated 5 months ago • prity6459

<div class="preformatted">Dear All, When using edgeR for differential expression of RNA-Sequences, I do not get any differentially expressed sequences (FDR <= 0.1). The R code...div class="preformatted">Dear All, When using edgeR for differential expression of RNA-Sequences, I do not get any differentially expressed sequences (FDR <= 0.1). The R...The 1st row is the seq…

edgeR edgeR

updated 12.0 years ago • Idit Buch

making a very silly mistake in my code somewhere? Thanks in advance for your help, Darya Vanichkina edgeR BCV plot (Disp = 0.0189 , BCV = 0.1375 ) http://i.imgur.com/Pf32qeBh.png edgeR smearplot http://i.imgur.com/bs6JyoEh.png DESeq...MAplot http://i.imgur.com/Ds9nfwth.png ## Sample code used # edgeR ----- row.names(counttable.sam) <- counttable.sam$Gene counttable.sam$Gene <…

PROcess edgeR DESeq PROcess edgeR DESeq

updated 11.2 years ago • Darya Vanichkina

I got totally confused when looking at edgeR manual somehow: The are different ways of estimating the dispersions (GLM and a classic approach). Also, one might estimate...y <- estimateGLMTagwiseDisp(y, design) </pre> what is quite weird because according to the edger manual they should give the same results

edger

updated 8.8 years ago • tonja.r

This is my first time using EdgeR or DeSeq2. I used HTSeq-Count to get counts for reads aligning to CDS (this is for ribosome profiling) for each gene. I obviously...aligning reads and reads that don't align to the feature (CDS). Should I remove these before running EdgeR or Deseq2?     &nbsp

edger deseq2

updated 5.8 years ago • cottrellka

4 normal tissues. I'm trying to do differential analysis. With the available read counts data using edgeR for differential analysis.  For the filtering steps I'm using this which is mentioned in edgeR tutorial <pre> keep

r edger differential gene expression filtering bioconductor

updated 6.4 years ago • Biologist

Hi all, I am using edgeR to do a differential expression analysis and several of the genes have FDRs reported as 0. My hopefully simple question

edger adjusted pvalue

updated 7.4 years ago • Nik McPherson

I have read the edgeR User's Guide, and Section 2.6 recommends setting a threshold of at least 5-10 absolute counts in a library to be considered

edger

updated 7.8 years ago • es874

Create a edgeR object for analysis dge <- DGEList(counts=countdata) ################Check how many genes have zero counts across samples ############ table(rowSums...Transform the data object for differential expression analysis##### logCPM <- cpm(dge, log=TRUE, prior.count=3) ########################################################################## ########### Differenti…

voom duplicateCorrelation() timeseries limma

updated 3.7 years ago • heikki.sarin

class="preformatted">Dear Bioconductors, I have an issue with calculating normalisation factors in edgeR. This has always i.e. on three other datasets worked just fine, which leads me baffled here. To summarise- -NaNs occur independently

Annotation edgeR Annotation edgeR

updated 12.2 years ago • Davenport.Colin@mh-hannover.de

measures RNA-seq analysis. This has been thoroughly answered through an extension of the edgeR manual section 3.5. However this has lead to me towards another question as I attempted to extend such...size in each group is different.  For example, here is a dataframe modified from the edgeR user manual concerning between and w…

edgeR

updated 9.8 years ago • Charles Determan Jr

Dear List, Our sequencing core recently switched from STAR to Kallisto. The genewise output was given as both TPM values and counts. Gordon Smyth has written that TPMs should not be used as input to EdgeR. In a recent paper (F1000 Research 2016,4:1521) Soneson, Love, and Robinson have presented evidence that the method they call simplesum_avextl for deriving reads-per-gene, from numbers-of-tr…

RNASeq-quantification edgeR TPM

updated 5.6 years ago • raf4

Hi, I would like to use edgeR to estimate the RPKM values.  I have (1) read counts files estimated by HTSeq-count, and (2) a transcript length file. I...Hi, I would like to use edgeR to estimate the RPKM values.  I have (1) read counts files estimated by HTSeq-count, and (2) a transcript length file. I know how to estimate CPM in edgeR, using below command lines. However, I do…

edger rpkm

updated 8.6 years ago • Gary

<div class="preformatted">Dear all, I'm trying to analyse an experiment from Small RNASeq (miRNA Seq). In this experiment I have 2 different types of mice (MT and WT) and a treatment variables (treated or cD and untreated or sD). So there will be 4 types of data : WTcD (treated WT), WTsD (untreated WT), MTcD (Treated Mutant) and MTsD (Untreated Mutant) So, my design is something likes thi…

RNASeq edgeR RNASeq edgeR

updated 11.3 years ago • Eduardo Andrés León

I would like some help getting DE genes from what is turning out to be a more difficult design than I thought. The data come from elsewhere, so the design isn't mine (nor can I just repeat everything). I want to get DE genes from different times in fetal mouse development (E14 and E16), so comparing 2 different gestational ages. I also want to look at fetal sex as a variable. My proposed analysis…

edgeR RNAseq voom variability estimator

updated 4.5 years ago • hcnbox

find out differentially expressed genes across all genotypes. Here is the code I am using. library(edgeR) y<-read.table('test_12339.txt' ) d <- DGEList(y, group = rep(1:3, each = 3), lib.size = lib.sizes) d <- calcNormFactors(d) times &lt

updated 13.5 years ago • Shreyartha Mukherjee

Hello, <span style="line-height:1.6">I am attempting to use edgeR (3.12.1)'s glmTreat() function </span><span style="line-height:1.6">to identify genes that are significantly up-regulated...by >2-fold in one group over another. My understanding from Sections 2.12 and 4.4.8 of the edgeR User's Guide is that the log2 fold changes for each gene will be tested again…

edger

updated 8.3 years ago • le2336

Gossner <a.gossner at="" ed.ac.uk=""> > To: bioconductor at stat.math.ethz.ch > Subject: [BioC] edgeR and FDR values always equals 1 > > Hi, > > While using edgeR to analysis my Tag-seq data, no matter which way I > analyse

edgeR edgeR

updated 13.9 years ago • Gordon Smyth

div class="preformatted"> after updating R and edgeR I lost the annotations in the final Diff.Expressed matrix (toptags) when running the edgeR pipeline. How do I get the row.names

edgeR edgeR

updated 11.1 years ago • Guest User

are generally recommended for most scenarios. However, there is an example in Section 4.10.3 of the EdgeR user's guide where these values are explicitly set in the function call: ``` keep.genes <- filterByExpr(y, group = y$samples...low? Additionally, when would you suggest modifying the default values? **Question 2** The EdgeR manual mentions that "*glmQLFit gives special attenti…

edgeR DifferentialExpression

updated 6 months ago • Jack S.

Hi, I am analyzing mRNA-Seq dataset using `EdgeR` package and testing filtering by `filterByExpr` and `rowSums` that would keep genes. I have question about interpreting...Histogram of average log2 CPM in EdgeR? I tested filtering in 4 different ways, and would like to know how to interpret the plot? Basically, `filterByExpr` looks

CPM filterByExpr edgeR histogram rowsums

updated 21 months ago • mohammedtoufiq91

div class="preformatted">I am using edgeR to look for differentially abundant ?segments? between two groups (data generated using high throughput sequencing...biological reps per group and a total of 18760 segments (83 rows with zero count are removed by edger). As a first approach, I used the common dispersion method and found the estimated common dispersion to be 0.135. After...I am using …

edgeR edgeR

updated 14.4 years ago • Ann Hess

Hi edgeR Users, I have employed edgeR to analyze RNAseq data before. Those data had two groups, one is control and one is treatment...Hi edgeR Users, I have employed edgeR to analyze RNAseq data before. Those data had two groups, one is control and one is treatment. However, now I need to investigate effect of chemical exposure on gene expression, so chemical exposure is a con…

edger

updated 6.3 years ago • ycding

Hi, Can a expressed gene dataset yielded after CPM be used in DESeq2 or EdgeR or the data should be completely raw count data? Thanks a lot for your kind help in advance

DESeq2 edgeR

updated 17 months ago • Sep

class="preformatted">Hi, Can you please tell me how the FC is calculated in the following test in edgeR? DrugvsPlacebo.1h = (Drug.1h-Drug.0h)-(Placebo.1h-Placebo.0h), Lana Schaffer The Scripps Research Institute Biostatistics

updated 10.7 years ago • Lana Schaffer

Hello, I am running a glm analysis with edgeR on 64 biologically independent samples, with 3 factors. I have sex (M and F), age (P0, P7, P15, P30), and genotype (Control, KO). I have

edgeR glm RNAseq

updated 4.0 years ago • jackiesalzbank

Hi, I'm having problems with the DGEList function in edgeR.  Here are the commands that I had input: library(edgeR) raw.data <- read.table(file = "Documents/.../myfile.csv", header

edgeR row.names DGEList

updated 9.6 years ago • ccheung

Hello, my sample sheet looks like this (RNA-seq): FACTOR BATCH factor1 run1 factor1 run2 factor1 run2 factor1 run1 factor2 run1 factor2 run2 factor2 run2 factor2 run1 factor3 run1 factor3 run2 factor3 run2 factor3 run1 factor4 run1 factor4 run2 factor4 run2 factor4 run1 so four conditions over two batches…

edgeR

updated 4.1 years ago • lexlogit

span style="line-height:1.6">RUVg uses the first call of edgeR to find the factors of unwanted variance. The design matrix is constructed with the possible batch effect variable...Trt2). Would it make sense to introduce it already in the design matrix and perform a first call of edgeR and  then RUVg

ruvseq

updated 8.8 years ago • tonja.r

reproducible code. I think however that you might be taking comments that were made in the edgeR User's Guide about an additive model and trying to apply them to an interaction model. Let me clarify. Your experiment...effect irrespective of genotype. This type of analysis is done in the last two case studies of the edgeR User's Guide: http://bioconductor.org/packages/2.10/bioc/vignettes/edge…

edgeR edgeR

updated 12.5 years ago • Gordon Smyth

<div class="preformatted">Hi all,- I want to compare logFC value from the output of exactTest function in edgeR for two different comparisons for each gene. So I have 4 conditions and I am testing if logFC for conditions 1 and 2 in that...preformatted">Hi all,- I want to compare logFC value from the output of exactTest function in edgeR for two different comparisons for each gene. So I…

updated 11.2 years ago • Alpesh Querer

Hi, I would like to install edgeR version 3.16.5. I am using following code to install, but getting a warning message.  Could you please help me? source

edger

updated 7.3 years ago • myprogramming2016

Hello, I am trying to do edgeR analysis, such as described in 3.5 of the [manual](https://bioconductor.org/packages/release/bioc/vignettes/edgeR/inst

edgeR design and contrast matrix

updated 7.1 years ago • b.nota