Bioconductor Forum

Could you let me know what is the default value (or recommended value) for thresholding the FDR in edgeR? Thanks, Son. [[alternative HTML version deleted]] </div

updated 10.1 years ago • Son Pham

Hi, I have a methylation dataset and it's single cell. I wonder how can I get appropriate values from the edgeR glmfit object for downstream clustering. This is what I've run: ``` design0 <- model.matrix(~0 + sample + celltype, data=file.df) design <- modelMatrixMeth(design0) y <- estimateDisp(y, design=design, trend="none") fit1 <- glmQLFit(y, design, robust=…

edgeR MethylationArray

updated 7 months ago • mico

data from a microorganism collected at different locations. I've been trying to perform an LRT using edgeR to test the location effect on transcription. What I want is to make a full model with all the coefficients, and compare...so <- sleuth_lrt(so, 'reduced', 'full') And wanted to make a similar test using edgeR. I would greately appreciate any insights

edger lrt

updated 4.8 years ago • arubio

external analysis, and I also see pseudo.counts numeric matrix of normalized pseudo-counts in your edger user guide. the word report in the accessory describe it more clearly Which kind of data in edger can be used for external...plot difference between groups. Urgent for help. 2. is there a detaied comparison of your edger with wilcox

edger normalization deseq2

updated 4.3 years ago • linouhao

find 'DGEList' BTW: I start the session by source("http://bioconductor.org/biocLite.R") biocLite("edgeR") biocLite("DESeq") Probably trivial, but help is still greatly appreciated. Thanks. jahn -- output of sessionInfo(): Error: could

updated 10.8 years ago • Guest User

Dear all, I analyzed a batch of samples using edgeR in order to isolate differentially expressed genes from a bacteria strain. Two experimental conditions were varying...like a batch-effect problem, what would be the best strategy for correcting it (if possible) before EdgeR analysis ? Is it a problem to have only a single temperature in common between batches ? I read about limma's "removeBat…

edger differential gene expression

updated 6.0 years ago • rfenouil

Hi everyone. I have been following a pipeline for RNAseq analysis using edgeR just until de point after performing a ExactTest. No my question is. Now i want to obtain the genes that are upregulated

RNAseq StatisticalMethod edgeR

updated 10 months ago • alvaroperona1

Is it possible to calculate a confidence interval on the log fold change reported in the output of edgeR? I suppose that knowing the number of reads in a gene and the tagwise dispersion one can find the total CV^2 for that gene

edgeR statistics confidence interval

updated 8.5 years ago • ri.lars

do not have any replicates for any of the conditions. **I am looking to perform an Anova test using edgeR**, to see the gene expression at different time points wrt sample 2 (as given). **Could anyone tell me the edgeR code I should...or estimate dispersion in this case. **I would be very grateful if someone could help me with the edgeR codes. Thank you

edger anova gene expression Dispersion

updated 5.2 years ago • ilovesuperheroes1993

Hi, We have airway epithelial models using 6 donors, including 4 female (two older and two younger) and 2 younger males. We've infected primary human bronchial cultures with the FLU virus. The transcriptional responses of these cultures were sequenced through RNA-seq at time intervals 6, 24, and 48 hr over 4 batches. This setup included some overlapping donors, as well as both technical and biol…

StatisticalMethod FoldChange edgeR RNASeq

updated 9 months ago • Sabiha

Hi, I am unsure as to whether the EdgeR normalization factors (calculated with calcNormFactors) take into account library size. From my reading, they only...with elsewhere but I unclear on this. Could someone please clarify the steps of normalization in EdgeR? Many thanks, Lucy

edgeR

updated 6.1 years ago • Lucy

I would like to compute the variance explained (i.e. coefficient of determination, R2) by a model in edgeR. Concretely, I am modelling various gene expression phenotypes using glmFit, and determining the significants of...I would like to compute the variance explained (i.e. coefficient of determination, R2) by a model in edgeR. Concretely, I am modelling various gene expression phenotypes using g…

edgeR

updated 2.4 years ago • Gemma

preformatted">i just killed some virus on my computer and met an very wired problem > library(edgeR) Error in get(".packageName", where) : cannot allocate memory block of size 3.5 Gb Error: package/namespace load failed for...edgeR? > sessionInfo() R version 2.15.1 (2012-06-22) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=Chinese (Simplified

updated 12.0 years ago • wang peter

Hi, I am not quite clear about the normalization in edgeR. I am not seeing any change in the actual read counts. They are same numbers except filtered for >10 reads, library size

edger rnaseq bioconductor

updated 8.6 years ago • myprogramming2016

<div class="preformatted">Hi, I have assembled 2 reference transcriptomes of the same species using a) genome-guided assembler on an incomplete draft-genome and b) genome-independent assembler. Q.1) Since, each assembly has it's own limitations making it difficult to combine the datasets, so I would like to know your suggestions for the two strategies: a) doing each differential expressi…

edgeR edgeR

updated 11.4 years ago • Eshita

I'm running an edgeR analysis on RNAseq data that was run in two seperate batches which I want to control for. Should the variable I'm interested...lt;- model.matrix(~group + batch)" or "design <- model.matrix(~batch + group)"? The edgeR manual says the group should go last, similar to DESEeq2, but I have been told by a collegue that it should go first

edger r

updated 5.0 years ago • lornaas

<div class="preformatted">Hi, I am using edgeR to detect differential expression in NGS experiments. I have a brief question on what I should considered as "total size...div class="preformatted">Hi, I am using edgeR to detect differential expression in NGS experiments. I have a brief question on what I should considered as "total

edgeR edgeR

updated 14.3 years ago • raffaele calogero

div class="preformatted">Hi everyone, I'm trying to use the goodTuring function in edgeR to estimate what kind of pseudocounts to use and I'm getting strange results with small number of categories: x<-c(312

Category edgeR Category edgeR

updated 12.1 years ago • Francois Pepin

Hi.  I am trying to figure out how to do an ANOVA like test with my data in edgeR. My data has 2 variables: treatment (2 levels) and time (5 levels).   I'd like to test for the effect of treatment, time...Something like y ~ time + treatment + treatment:time I can see two possible ways to do this in edgeR: 1) combine treatment and time into a single factor and then te…

edger main and interaction effects edger r edger de

updated 8.8 years ago • julie.green

Dear Sir/Madame, I am using the EdgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html[)](#EdgeR) - processAmplicons function just to raw count...Dear Sir/Madame, I am using the EdgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html[)](#EdgeR) - processAmplicons function just to raw count the number of sgRNAs I have in samples treated with custom-made sgRNA/CRISPR …

EdgeR CRISPR Barcode processamplicons

updated 6.3 years ago • neggersjasper

I have read posts were counts of technical replicates are merged before starting the DEG analysis in edgeR, but this was in cases where technical replicates referred to identical libraries being run many times. Unfortunately...those that were under the threshold in order to have a final biological replicate as an input in edgeR. My **second** question would be: Could I get any comments on this l…

edgeR

updated 3.5 years ago • mo17

Hi, I would like to know if it is possible to use EdgeR for differential expression analysis starting from data that are no raw count, but are normalized counts. I just try

r edger de

updated 9.5 years ago • aiko

Hello there, How can we find the normalized count from the count data in edger? It seems there are two opposite ways to derive normalized count from the count data. 1. normalized counts=counts*norm.factor

edger

updated 5.2 years ago • mzillur

Hi everyone,  I have been analyzing genetic screen data with edgeR for years -- my favorite toolbox! Now I was hoping to get people's opinions about a special case: analysis of bottlenecked...c(1, 0, 0, 0, 50, 0)  I have recently been analyzing data like this with the standard edgeR pipeline (with and without using calcNormFactors) in conjunction with the Camera function to sc…

edgeR

updated 6.2 years ago • knaxerova

doing the batch correction, or shall you have any suggestions, please let me know ;) <code>library("edgeR")<br/> eset <- read.delim("RNAseq",row.names="Geneid")</code> <code>group <- factor(c("wt","wt","wt","ko","ko","ko"))<br/> group <- relevel(group,ref...calcNormFactors(y) `` `` ### MDS before batch correction `` <code>logCPM &…

limma edgeR

updated 7.6 years ago • Bogdan

I'm doing a pairwise comparison (classic two groups comparison in EdgeR) and wonder if I should do an additional permutation test? It means, randomly permute the labels in these two groups and...I'm doing a pairwise comparison (classic two groups comparison in EdgeR) and wonder if I should do an additional permutation test? It means, randomly permute the labels in these two groups and find DE gen…

edger

updated 9.7 years ago • Son Pham

I use edgeR for mRNA analysis and I want to see the difference in BCV between the control group and the treated group. I see that there

edgeR

updated 4.6 years ago • viktoria.c.karlsson

I'm performing quantile normalization with CQN and then using edgeR on some ATAC-seq samples I have and I'm trying to understand/determine the following: When setting the values for library

CQN atac-seq normalization edgeR

updated 6.4 years ago • shankasal

I have whole exome sequencing data from insect individuals from two different populations. I'm interested to see if there are any genome regions that have much better coverage in one population than in the other. (For example, I want to see if the exome capture probes work much better for one population, or see if there are any large deletions.) Would there be any problem, conceptually, with usin…

edgeR exome

updated 5.4 years ago • am3

glmFit/glmLRT or glmQLFit/glmQLFTest, I should use for DE gene analysis in paired designs using edgeR. In the edgeR Users Guide (rev 20.4.2016),  glmFit/glmLRT is used in Chapter 3.4.1 and 4.1 for paired designs, whereas...published in Methods Mol Biol (vol 1418, pp391-416, 2016) about Quasi-likelihood methods in edgeR, but there was no mention paired designs in the pap…

edger paired samples glm QL F-test LR-test

updated 8.1 years ago • Akira Imamoto

edgeR. I likewise found that edgeR yielded more differentially > expressed tags or genes. I know Dr. Gordon Smyth mentioned...the model comparison used in > both programs is below (and below that if helpful, full code for edgeR > -- I am using the newest release). I assume the differences are coming > from the ways DESeq and edgeR estimate dispersion...I am glad to hea…

GLAD edgeR DESeq GLAD edgeR DESeq

updated 12.8 years ago • Gordon Smyth

Dear reader I am using edgeR to do differential gene expression analysis on my mRNA seq data. I just have two group, each of 5 replicates, that I want...to compare. Out of curiosity I performed both the classic EdgeR (exact test) and the GLM (glmQlFtest) approaches. Surprisingly, I got really different results, the exact test gave me 192

DifferentialExpression edgeR

updated 9 months ago • Jurgen

<div class="preformatted">Hello edgeR maintainers, I just ran into an error with code that is several weeks old. I cannot subset my DEGList object anymore. I created...div class="preformatted">Hello edgeR maintainers, I just ran into an error with code that is several weeks old. I cannot subset my DEGList object anymore. I...0 rows, data has 1 The code worked a couple of weeks ago. I …

edgeR edgeR

updated 10.1 years ago • Katja Hebestreit

are cpm normalized values? des <- model.matrix(~KRAS) fit <- glmFit(y2, des) __lrt <- edgeR::glmLRT(fit)__ &nbsp

edger r

updated 9.2 years ago • R

I was wondering whether anyone could shed light on this discrepancy I observed between two different edgeR versions. I used a version 3.12.1 of edgeR and did all my gene set enrichment analysis with it, but recently I updated the...edgeR version to 3.18 and realised that the p-values that were generated from using kegga() are different when v3.18 was used...test.  There was no differen…

edger kegga

updated 7.2 years ago • cronanz

while the tumor subtypes I am working with have measurements ranging from 80 to 140 samples. Is EdgeR (or any other equivalent package) an option or I cannot get significant results from this kind of analysis? I know that...group sizes are not required to be the same in EdgeR, but is a comparison between 41 and 141 samples reliable? Thank you in advance. R

edger differential gene expression rnaseq

updated 6.0 years ago • rina

files and followed the steps as mentioned in the trinity tutorial but somehow getting this error in edgeR. ``` Error, cmd: R --vanilla -q < matrix.counts.matrix.align_estimate_rsem_P3_vs_align_estimate_rsem_unP3.align_estimate_rsem_unP3.vs.align_estimate_rsem_unP3...trinityrnaseq-2.2.0/analysis/diffenetialexpression/run_DE_analysis.pl line 712. WARNING: This EdgeR comparison faile…

edger

updated 5.4 years ago • sakshi.rajput55

Hello, I'm trying to create a design matrix using edgeR or DESeq2. I have a time course experiment with includes different does of a drug and different cell lines. For each cell

edgeR DESeq2 RNASeq

updated 3.7 years ago • kimmcl860

<span style="line-height:1.6">I am reading the latest version of edgeR user guide (</span><a href="https://mail.mssm.edu/owa/redir.aspx?C=IR7uVkR_fkKbMz-ifqAaCEyqCCRQQdMI1IKcHi8I32R3DXlepKAZ4eRpKiW2zaqSjuH8UxEeFjs.&URL=https%3a%2f%2furldefense.proofpoint.com%2fv2%2furl%3fu%3dhttps-3A__www.bioconductor.org_packages_3.3_bioc_vignettes_edgeR_inst_doc_edgeRUsersGuide.pdf%26d%3d…

edgeR

updated 8.6 years ago • yifan.mo

Dear list, I am analyzing a multi-factor time course RNA-Seq experiment with batch-effects using edgeR. After I perform a glmLRT, I cannot use topTags to display the most significant DE tags if I passed contrasts. Here's what...function I don't know if this is the expected behavior (I would say no). I browsed a bit the edgeR source code. Here's what I believe might the culprit : In glmFit.R :…

Cancer edgeR Cancer edgeR

updated 11.8 years ago • h.soueidan@nki.nl

<div class="preformatted">Hi Gordon, I've been trying to use edgeR to analyze some mRNA-seq data. I've begun looking at a data set where the cells are either unstimulated or stimulated with...div class="preformatted">Hi Gordon, I've been trying to use edgeR to analyze some mRNA-seq data. I've begun looking at a data set where the cells are either unstimulated or stimulated...are: 26693…

Sequencing graph edgeR Sequencing graph edgeR

updated 11.9 years ago • Thomas Frederick Willems

values column from `Deseq2` results to rank the genes for gene set enrichment analysis. With `edgeR` I use the following code. fit <- glmQLFit(y, design, robust=TRUE) contrast.matrix <- makeContrasts(Tumor-Control, levels...glmQLFTest` I have the `Fstat` in the results. But, I want to get t-statistic values column using `edgeR` to rank genes based on that column and u…

r edger t-statistic fgsea gsea

updated 5.4 years ago • Biologist

<div class="preformatted">Dear edgeR community, Good day. I can learn summary of the up and down regulated genes/tags from >summary(de <- decideTestsDGE(lrt...div class="preformatted">Dear edgeR community, Good day. I can learn summary of the up and down regulated genes/tags from >summary(de <- decideTestsDGE

edgeR edgeR

updated 12.3 years ago • KJ Lim

I have used the exact test in edgeR to compute the log fold changes. Here is the snippet: <pre> d <- DGEList(counts=counts, group=samples$Condition...division by zero). Yet the FC is reported as being ~2^-9. My question is - how does edgeR come up with this value? I've checked both the manual and the reference guide but couldn't…

edgeR

updated 9.7 years ago • Nick N

Hi, i am using edgeR for differential expression study. I am providing raw read counts. In few cases i am getting logFC is negative even if

edger

updated 5.4 years ago • Neu.S

Hi all, I am using edgeR to identify genes differentially expressed in my experiment. I have cells which were grown in 4 different cell media...media1 vs media3; media1 vs media4; media2 vs media3....). I have been reading the manual for edgeR and this is my code: ``` > library(edgeR) Loading required package: limma > library(statmod) > rawdata <- read.delim…

edger error

updated 5.4 years ago • lucap

Hello all, We have two variables from RNA-seq data: tissue (tissue1 and tissue2) and treatment (healthy and unhealthy). There are in total 4 healthy and 4 unhealthy animals, from which samples from tissues 1 and 2 were collected from each animal. We would like to perform a differentially expression gene analysis between healthy and unhealthy animals, considering the tissue effect (both tissues) …

edger deseq2 rnaseq differential gene expression

updated 5.9 years ago • camilla.alves

gt;>> But how to get the counts after TMM and lib.size normalization ? >> >> The edgeR user's guide says: >> >> "The edgeR methodology needs to work with the original digital expression counts, so these...at 10:58, Fran?ois RICHARD wrote: >> >>> Dear all, >>> I am using Ed…

Normalization edgeR Normalization edgeR

updated 12.1 years ago • Mark Robinson

div class="preformatted">Hello Bioconductor mailing list, I'm using edgeR to analyze RNA-seq and RIP-seq data. I'm using the moderated gene-wise dispersion method where I choose a prior.n based

edgeR edgeR

updated 10.6 years ago • Jason Miller

Hi! I am doing a DE analysis with DESeq2 and EdgeR (glm approach). For EdgeR I filter with a minimal proportion of 80% (0.8) and minimal counts of 1 keep <- filterByExpr(y, group

DESeq2

updated 6 months ago • fr8712ca-s

<div class="preformatted">Dear Bioconductor list, I'm try to get differentially expressed genes from two groups of samples using EdgeR. In the first group I have only 1 sample and in the second there are 3 biological replicates. (I will get more samples per group in the future but for now I have to make an analysis pipeline with only that 4 samples) The sample came from a metatranscriptomi…

edgeR edgeR

updated 11.3 years ago • Amos Kirilovsky

hi, when I using edgeR to identify differentially methylated regions (DMR) between different groups with edgeR guidepaper, I have a question...methylation level between the 60-65 and the 40-45 µm groups. \#\#\#\#\#\# the contents above from edgeR guide, my question is how to to design the contrast column like 8th column.   &nbsp

edger methylation

updated 6.0 years ago • sgld

Hi, I'm using edgeR to analyze a RNAseq data set which has many biological replicates and several variables. I have tried to use both the...more appropriate for my data set?  2. I noticed that by updating R to the 3.3.1 version and edgeR to 3.14 version the results of the glmQLFit are different from the ones obtained with R 3.2.2 and edgeR 3.12 version

edger rnaseq glm glmfit

updated 8.2 years ago • alessia.donato

each read, normalized by gene length and alignment quality. There's a lot of posts stating that EdgeR and DESeq2 should (usually) only be used on raw counts, but that is in the context of standard transcriptomics workflows...would it be appropriate to use the humann2 output for differential abundance analysis with EdgeR or DESeq2? What if the data was just normalized by alignment quality but no…

edger deseq2

updated 6.8 years ago • nyoungb2

read number for a specific sample (e.g 20million) as the y$samples$lib.size when I am using edgeR, or shall I let edgeR do it automatically (as far as I understand, edgeR will automatically sum all reads in the DGElist...will also affects the y$samples$norm.factors. (y <- calcNormFactors(y)). If I let the edgeR do it automatically, the norm.factors will be only take into considera…

edger

updated 8.0 years ago • wbli2012

Hi, I used STAR, featureCounts, and edgeR for RNA-Seq alignment, quantification, and differentially expressed analysis. Could you teach me how to change sample

featurecounts edgeR

updated 6.3 years ago • Gary

div class="preformatted"> Dear community, I use edgeR to do the data analysis of my RNA-seq project (as mentioned in my previous posts about multi-factor analysis of RNA-Seq

edgeR edgeR

updated 10.4 years ago • Guest User

design has the form of a one-way layout, so you could >> analyse your data using classic exact edgeR instead of the glm code. >> In this style of analysis, you would make pairwise comparisons between >> the time points...csm29 at="" duke.edu=""> >>> To: bioconductor at r-project.org >>> Subject: [BioC] edgeR gl…

GO GLAD edgeR GO GLAD edgeR

updated 13.6 years ago • Gordon Smyth

as minor and 30 as major histopathologic responders (TRG1-2 and TRG4-5 respectively). I have done edgeR and wilcoxon test to find genes driving the difference of tumor samples of patients with major or minor response as...Switch to the classic mode. > sqrt(y$common.dispersion) [1] 0.6280918 > EdgeR <- exactTest(y) > topTags(EdgeR) Comparison o…

edgeR r wilcox RNA-seq cancer

updated 5.6 years ago • Fereshteh

Just to follow up here: yesterday I committed an update to the release and devel versions of edgeR to fix a big related to the use of offsets in the GLMs. I strongly recommend that you and other edgeR users update to the...convergence checking etc, that should solve the problem. This will be incorporated into the edgeR package during the next week. >> >> Regards &…

RNASeq edgeR RNASeq edgeR

updated 13.8 years ago • Davis McCarthy