Bioconductor Forum

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 7.5 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 10.4 years ago • Nick N

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 7.5 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 9.0 years ago • gregory.l.stone

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 9.7 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 3.2 years 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 4.6 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 6.5 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 12.9 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 9.2 years ago • romsdahl

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 8.1 years ago • Ekarl2

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 8.4 years ago • Jack

hi buddies! i´m trying to normalize my count reads in Rstudio with EdgeR plugin usin the TMM method by now i just got the TMM factors, but then, what is the next step? i ran: pr = read.csv("feature_counts.csv

Normalization edgeR

updated 3.8 years ago • kevin

Dear, I have been using edgeR for many years, and there is a problem that always confuses me. Just have a look at this experimental design ( control: replicate1

edgeR

updated 5.9 years ago • wangjiawen

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 10.1 years ago • Ekarl2

preformatted">Dear all, 1) GLM & residuals: I have a question concerning the use of GLMs in edgeR and the analysis of the residuals after model fitting. I have followed all the steps until model fitting, e.g.: glmfit.D

edgeR edgeR

updated 14.0 years ago • Susanne Franssen

if it is a good idea to do not take into account replicate "C1" for downstream analysis or, however, edgeR is able to compensate to this 'outlier'? Thanks in advance, Antonio <img alt="" src="http://i.imgur.com/wygoBtF.png" style="height

edger DEG mds plot

updated 8.5 years ago • baus87

Hello everyone: I used the glmQLFTest function by edgeR to detect differentially expressed genes. I have ONE dataset and two gene lists: (1) all genes (2) genes remained after removing

glmQLFTest edgeR

updated 3.8 years ago • Pei

I have used edgeR and limoRhyde to predict differential expression in a circadian experiment. Below ZT\_cos and ZT\_sin is sin and cos

edgeR circadian rhythms limorhyde

updated 7.3 years ago • ri.lars

I'm attempting to use edgeR to analyse my RNA-seq data.  I have managed to use readDGE to create a data object which I have called DG and it looks...expression values with these meta tags i.e. non-aligned features.  Secondly, in accordance with edgeR's recommendations I wish to remove features which do not have at least 1 read per million in n samples, where n for my dataset...n…

edger filtering cpm

updated 9.5 years ago • lynski008

I have two questions regarding the cpm filter suggested for edgeR: <span style="line-height:1.6">1.</span> I am confused by the statement from the documentation "As a rule of thumb, genes are kept...I have two questions regarding the cpm filter suggested for edgeR: <span style="line-height:1.6">1.</span> I am confused by the statement from the documentation "As a rule …

edger cpm multiple factor design independent filtering

updated 10.1 years ago • dietahanson

Dear, I am using the (robust) QL pipeline in edgeR with following lines of code > estimateDisp > glmQLFit I understand that with this pipeline, only the NB trended...Dear, I am using the (robust) QL pipeline in edgeR with following lines of code > estimateDisp > glmQLFit I understand that with this pipeline, only the NB trended dispersion

edger

updated 9.1 years ago • veronique.storme

This is an easy question but I can't find good documentation.  After installing  or "sourcing" biocLite and installed relevant packages (edgeR, etc) I can run my analyses. But after closing the R session, and then restarting it, I have to resource BiocLite and then load...documentation.  After installing  or "sourcing" biocLite and installed relevant packages…

edger bioclite installation

updated 10.6 years ago • lplough

div class="preformatted">Dear edgeR authors and users, I am using the currently-released version of edgeR, edgeR_2.6.0. When I tried to estimate common dispersions

Cancer edgeR Cancer edgeR

updated 13.9 years ago • Yao,Hui

differential expression tests. For more complex experimental designs, would it be reasonable to use edgeR's GLM method to call DE genes from dge objects containing voom transformed counts

limma voom edger rnaseq

updated 10.0 years ago • adam.p.taranto

Hi, I am using edgeR to analyze differential expression of my RNA-Seq data. I am getting a plot of log-fold change vs log-counts per million

edger

updated 9.4 years ago • linya

I followed the same steps with my data. library(limma) library(Glimma) library(edgeR) mycpm <- cpm(U) head(mycpm) thresh <- mycpm > 0.5 head(thresh) keep <- rowSums(thresh) >= 2 table(keep) summary(keep) counts.keep...I also tried using edgeR with the same data. I used the same code mentioned in edgeR tutorial for differential expressi…

limma edgeR differential gene expression r

updated 8.5 years ago • Biologist

the names of all required packages     package <- c( 'AnnotationDbi', 'caTools', 'edgeR', 'GenomicRanges', 'GenomicAlignments', 'gtools', 'Rsamtools', 'VennDiagram' )           \# Install required...packages, but some packages are problematic, giving me error messages of this kind: pack…

edgeR packages

updated 11.0 years ago • Patrick Schorderet

B + C  + A x B   + A x C  + B x C + A x B x C  Can DESeq2 or edgeR fit the mixed model? Thanks. When I searched "DESeq/DESeq2/edgeR random effect", I found this post: <http://seqanswers.com/forums

deseq2 edger

updated 9.7 years ago • Yanzhu Lin

div class="preformatted">Dear edgeR users, Contrary to expectation, when I filter out tags with with low counts in edgeR I get fewer genes that are differentially...many individuals of one group having cpm < 1. Or could this somehow be an artifact of how I ran edgeR? On perhaps a related note, should I alter my code because I have a fairly large number of biological replicates. Below

edgeR edgeR

updated 13.1 years ago • Mark Christie

be modified in the typical workflow and so goes unmodified. An alternate entry point to this is via EdgeR for DGE objects, via a `` plotMDS.DGElist `` handler. From the [source code](https://github.com/Bioconductor-mirror/edgeR/blob

limma edgeR

updated 8.5 years ago • andrew.lonsdale

span> Currently there are (to my knowledge) two different ways of calling the same functions: using edgeR's implementation directly on a DGEList or first transforming the data with voom, and then use standard limma. In some...from the two - I'm wondering what's currently considered best practice when choosing between the edgeR and the limma+voom implementation? Are there any important statis…

limma edger mroast romer camera

updated 10.0 years ago • maltethodberg

Hello Gordon,   I am using edgeR to do pairwise comparison for 3 conditions. The avg values for each condition are:   AVG\_C1 : 1596 AVG\_C2: 1354 AVG\_R

edgeR

updated 9.8 years ago • sharvari gujja

Hello, The question I would like to ask is : Using edgeR's GLM methode nested interaction between two explaining variable, one continous variable (unlinked to genotype), the

edger rna-seq

updated 6.3 years ago • chapdelainev

nbsp; Hi, I am trying to use edgeR for analysis of gene expression across 4 RNASeq samples(different stations) (3 replicates each.  The information

edger differential gene expression GLM Tutorial

updated 9.9 years ago • wendy_11

may stray toward being a general statistics question, but given that it involves tests conducted in edgeR I thought it would still be appropriate to post here (please let me know if that is not the case) in case there is a mistake...methods. I am analyzing an RNA-seq dataset with three factors: genotype, sex, and age. I am using edgeR to identify DE genes and alternatively spliced genes. My quest…

edgeR

updated 2.4 years ago • jbono

Hi everyone,  I am wondering about the edgeR normalization step (calcNormFactors) for CRISPR screens. The edgeR user guide says that TMM normalization is recommended...of normalization (if any) should/could be applied? What is the best way to set up the analysis in edgeR in such situations? Any thoughts would be much appreciated! Thank you.  Kamila

edger calcnormfactors

updated 8.3 years ago • knaxerova

Dear colleagues: I am analyzing the result of some cancer samples miRNA NGS experiments with edgeR, with the following setup: R version 2.15.3 (2013-03-01) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=Italian_Italy.1252

Cancer edgeR Cancer edgeR

updated 12.8 years ago • alessandro.guffanti@genomnia.com

in trying out a tutorial with example data using the shRNAseq tool (which has been integrated into EdgeR) . The tutorial is here: http://bioinf.wehi.edu.au/shRNAseq/pooledScreenAnalysis.pdf.  There are some example

shRNAseq edgeR shRNA

updated 10.4 years ago • K

<div class="preformatted">Dear List, I am also trying edger on my data (3 groups, 2 reps each). Bacterial samples. design condition pair 1 Cont 1 2 Cont 3 3 Trt1 1 4 Trt1 3 5 Trt2 1 6 Trt2 3 However...div class="preformatted">Dear List, I am also trying edger on my data (3 groups, 2 reps each). Bacterial samples. design…

edgeR edgeR

updated 12.8 years ago • Natasha

bioconductor for more powerful analysis. We have many RNAseq libries with out replicates. And I read edgeR document and understand, not much use of doing any significant analysis. But, now, we are in a position to have biological

RNASeq Organism edgeR RNASeq Organism edgeR

updated 13.8 years ago • gowtham

experiment comparing responses to a drug treatment (trt, ctrl) in two populations (A, B) using both edgeR and DESeq2. Sequences for all four treatment\*population group combinations were generated simultaneously in a single...and B on a different run, and thus that batch effect would need to be included in linear models for edgeR and DESeq2. But I'm having a difficult time figuring out how batch …

rnaseq batch effect deseq2 edger

updated 7.3 years ago • rproendo

if it's possible to incorporate the weights calculated by voomWithQualityWeights() in glmQLFit in edgeR. My code is as follows: v <- voomWithQualityWeights(dge, design, plot=FALSE) qlfit\_weigthed <- glmQLFit(dge$counts, design

edger limma-voom voom

updated 9.0 years ago • gregory.l.stone

I have a analysis in edgeR, but it ended by error. This is my data: Sample treat factor1 factor2 s1 CT 1 c1 s2 CT 1 c1 s3 CT 2 c1 s4 CT 2 c1 s5 CT 1 c2 s6 CT 2 c2

edgeR methylation

updated 2.1 years ago • sat

I have a analysis in edgeR, but it ended by error. This is my data: Sample treat factor1 factor2 s1 CT 1 c1 s2 CT 1 c2 s3 CT 2 c3 s4 CT 2 c4 s5 CT 1 c2 s6 CT 2 c3

edgeR

updated 2.1 years ago • sat

I have a analysis in edgeR, but it ended by error. This is my data: Sample treat factor1 factor2 s1 CT 1 c1 s2 CT 1 c1 s3 CT 2 c1 s4 CT 2 c1 s5 CT 1 c2 s6 CT 2 c2

edgeR

updated 2.1 years ago • sat

Hello, I have inherited a table of differential expression results from edgeR (with logFC, logCPM, LR, PValue and FDR). Unfortunately, I do not have access to the original gene counts. I would like to perform

limma camera cameraPR edgeR gene set testing

updated 7.5 years ago • jamie.gearing

Hi. I have a problem about different DEG result from analysis same data using DESeq2 and edgeR. Here is two raw all DEG result without fiter based on |logFC| and padj/FDR ``` # DESeq2 23000 gene baseMean log2FoldChange...Hi. I have a problem about different DEG result from analysis same data using DESeq2 and edgeR. Here is two raw all DEG result without fiter based on |logFC| and padj/FDR `…

DESeq2 edgeR

updated 6.4 years ago • 15958021290

Starting from featureCounts generated raw counts file, I used edgeR to estimate the DE analysis and it went well. Now I use CPM normalized files to explore some specific genes expression...can I get input gene length to rpkm() function. This [discussion][1] tells that recent version of edgeR can directly find gene length from DGEList object. I am using edgeR_3.28.1 and can anyone direct me how to…

Normalization edgeR RPKM

updated 5.3 years ago • anikng

<div class="preformatted">Hello all, Im currently using EdgeR to analyze RNASeq data and have very much appreciated the software and its incredibly helpful user manual. More specifically, I have two questions. The first is whether I have chosen the correct method for analyzing my multi-factorial experiment. I have 2 factors, state (apo, sym) and treatment (control, treatment). Im inte…

RNASeq edgeR RNASeq edgeR

updated 12.9 years ago • Morgan Mouchka

Dear all, I am currently using the edgeR package for my research on 16S RNA metabarcoding. At the moment, I am focusing on TMM normalization, and I am quite...confused by the way people use the calcNormFactors function. Indeed, in the edgeR vignette, it is written : _" The normalization factors of all the libraries multiply to unity. A normalization…

edger normalization

updated 7.3 years ago • Pauline

Then rounded off the expected read counts to use for differential expression analysis using edgeR at both transcript and gene level. However, I found that the number of DE transcripts were almost 10 times less than those

edgeR edgeR

updated 12.5 years ago • Alan Smith

<div class="preformatted">Hi all, I'm using edgeR for multiple groups comparison. I have two treatments (WT and mutant), each treatment in three tissues (root, leaf, seed), each...div class="preformatted">Hi all, I'm using edgeR for multiple groups comparison. I have two treatments (WT and mutant), each treatment in three tissues (root, leaf, seed

edgeR edgeR

updated 14.3 years ago • Xiaohui Wu

<pre> This is a head of my dataset, with expected counts from RSEM, with 3 biological replicates of 2 samples (control and treatment), as can be seen in the group variable below. > head(rsem, 10) X4_7 X7_9 X8_13 X7_10 X4_27 X5_25 comp0_c0_seq1 0 0 0 0 0 0 comp100001_c0_seq1 0 1 3 2 1 1 comp100006_c0_seq1 2…

edger

updated 10.9 years ago • cpcantalapiedra

Dear edgeR users or developers, I am trying to understand the order of calculations in the latest QL workflow Comparing the source

edger

updated 10.2 years ago • veronique.storme

Dear All, I am running a differential expression analyses in E using EdgeR packge, and before that I would like to detect which of my samples is an outliers to remove them. I have actually formed

edgeR

updated 3.8 years ago • Mohamed

I'm trying to add gene annotation to my DGEList object in edgeR package but it giving me error as following: ``` Error in .testForValidKeys(x, keys, keytype, fks) : None of the keys entered are

edgeR DEG

updated 6.4 years ago • mjavad2012

than one control, these controls are \_not\_ technical replicates. Will this be an issue for an edgeR-based differential expression analysis? It appears that "control" is unevenly represented in the different batches

edgeR batch effect

updated 10.0 years ago • Ekarl2

Check dimensions again to see effect of filtering dim(rawdata) ################# # Running edgeR # ################# # load edgeR library('edgeR') # make class labels class <- c( rep("TM",3), rep("Mock",3) ) #Get common gene names #Gene=rownames(rawdata) #Symbol

edgeR

updated 3.8 years ago • venura

Hello, I am trying to make a smear plot with edgeR to look at and RNA-seq data set that has no statistically significant differentially expressed genes. When I plot this

edgeR plotSmear

updated 3.1 years ago • Tess