Bioconductor Forum

div class="preformatted">I am experimenting with edgeR for high throughput (next gen) sequence data and proteomics spectral count data and have a few questions. 1. Is it correct...the pseudocounts (pseudo.alt produced by estimateCommonDisp) as normalized counts? According to the edgeR vignette ?The pseudocounts are calculated using a quantile-to-quantile method for the negative binomial so …

Proteomics graph edgeR Proteomics graph edgeR

updated 14.5 years ago • Ann Hess

y$counts-floor(y$counts)) [1] 0 I have also posted the session information as below. Both the R and edgeR package are the most recent versions. However, the results are still the same as before. Are there other possible reasons...max(y$counts-floor(y$counts)) It also isn't clear that you have installed the current version of edgeR. Have you installed R 3.1.0? Can you please give the sessionIn…

edgeR edgeR

updated 10.4 years ago • Guest User

that are not sufficiently expressed y <- edgeR::DGEList(counts=Y) y <- edgeR::calcNormFactors(y) edgeIt <- function(group) { nr.states <- length(unique(group)) group <- as.factor...f <- stats::formula("~group") design <- stats::model.matrix(f) y <- edgeR::estimateDisp(y, …

edgeR

updated 6.1 years ago • Ludwig Geistlinger

<div class="preformatted">Dear Bioconductor Authors, I fitted a generalized linear models using glmFit() in edgeR. I wanted to extract the estimated fisher information matrix (or the estimated inverse fisher information matrix) from the fitting. The function approx. expected.info() in edgeR seems to be the right function to use. However, I have two problems when using it: (1) It does not w…

edgeR edgeR

updated 11.9 years ago • Ji, Tieming

understand the choices when using qunatification pseduoaligners like Kallisto for per-gene estimates. EdgeR official documentation mentions that we can use Tximport "which produces gene-level estimated counts and an associated...edgeR offset matrix". In another place I read that EdgeR ignores estimated normalization factors if it detects provided offsets

edgeR DifferentialExpression

updated 3.9 years ago • ognjen011

Hi everyone, I am trying to install edgeR on my M1 Mac, however I got this error: ```r Loading required package: limma Error: package or namespace load failed for ‘edgeR...unable to load shared object '/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/edgeR/libs/edgeR.so': dlopen(/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/edgeR/libs/edgeR.so, …

edgeR

updated 21 months ago • Onur

<div class="preformatted">Dear Daniel, The guidelines are the same for miRNA-seq as for RNA-seq. At its simplest, you simply need a reasonable minimum number of counts in at least some samples. At a minimum, I think you would want at least 5 counts, maybe more, in each sample in which the gene in expressed. So, if your sequencing depth is about 20 million reads per sample, you might ask…

Sequencing miRNA edgeR Sequencing miRNA edgeR

updated 10.3 years ago • Gordon Smyth

<div class="preformatted">Dear Edger developers and users, I would like to compare transcription levels of orthologous genes belonging to different species, in order to find significant species-dependent changes in transcription levels. I though of using Edger for such analysis. Specifically, I have the read-counts data for several RNA-Seq samples, for 2 different species (e.g., read...di…

Transcription edgeR Transcription edgeR

updated 10.1 years ago • assaf www

<div class="preformatted">Dear edgeR Users, I have RNS-Seq count data by genes, 4 treatment groups (each with 2 biological replicates) and two factors (E: C or H, and...div class="preformatted">Dear edgeR Users, I have RNS-Seq count data by genes, 4 treatment groups (each with 2 biological replicates) and two factors (E: C or H...A: 13 or 25). And I applied the GLM model of edgeR with …

Regression edgeR Regression edgeR

updated 11.6 years ago • Ari Eszter

<div class="preformatted"> Hi, I have been working with edgeR to find differentially expressed genes for RNA-seq data. I have been working with a data set with 3 treatment groups and...div class="preformatted"> Hi, I have been working with edgeR to find differentially expressed genes for RNA-seq data. I have been working with a data set with 3 treatment groups...The samples were sequen…

edgeR edgeR

updated 11.1 years ago • Guest User

Hi, in edgeR how can I write the FDR values to DE file? et <- exactTest(dgelist) fdr <- p.adjust(et$table$PValue, method="BH") I know exactTest

rnaseq edgeR

updated 2.4 years ago • edusbioinfo

Thanks for preparing the guideline on edgeR. However, I did not see any information supporting continuous variables in edgeR. May I know does edgeR supporting below

edgeR

updated 3.9 years ago • Ivy

div class="preformatted"> How suitable is edgeR for analyzing RNA sequencing data obtained from multiple studies, possibly using multiple platforms? I am trying...RSEM-processed data for cancer-specific sub-projects (each with 200+ samples). I am trying to use edgeR for differential expression analyses with Exact test, using 'raw count' values in the two cancer data-sets as the input...for e…

Sequencing Cancer edgeR Sequencing Cancer edgeR

updated 11.5 years ago • Guest User

working on RNA-seq data. I am trying to go through a differential gene expression analysis using EdgeR and starting with 2 conditions * 2 replicates = 4 runs (illumina, mapped with bowtie on known reference genome). I have few...exactTest() run the differential analysis (performing negative binomial test). But according to the edgeR manual, those two functions called the equalizeLibSizes() functi…

Normalization GO edgeR Normalization GO edgeR

updated 12.2 years ago • François RICHARD

div class="preformatted">Hi, I would be grateful for some input on using edgeR for small RNA sequence data. I have been testing edgeR on a set of miRNA data (3 groups with n=10, 15 and 15). After removing genes

miRNA edgeR miRNA edgeR

updated 13.0 years ago • Helena Persson

div class="preformatted">Hi there, I'm an amateur edgeR user, and I'm having trouble generating a heat map for the differentially expressed genes. All examples that I've looked

edgeR edgeR

updated 10.5 years ago • Eleanor Su

<div class="preformatted">Hello, I have used edgeR for DGE analysis and also generated plotSmear. I guess by dufault the plotSmear shows red dots for differentially expressed...div class="preformatted">Hello, I have used edgeR for DGE analysis and also generated plotSmear. I guess by dufault the plotSmear shows red dots for differentially

edgeR edgeR

updated 13.4 years ago • Sridhara Gupta Kunjeti

Hi there, Would anyone know the correct way to create a citation for [edgeR user manual][1] ? I wasn't sure whether to cite the original edgeR paper or if the user manual needs a separate citation? Thanks...1]: https://www.bioconductor.org/packages/devel/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf

edgeR

updated 4 months ago • k___

I am so new in using R and edgeR. I calculated the logFC in edgeR using the following code: ``` targets <- read.delim("cell_line_M.txt", stringsAsFactors...the strategy suggested in [here][1] like: FC=sqrt(8*7)/ sqrt(7*4) --> logFC=log2(FC) = 0.49 but edgeR suggest logFC=0.2 Can anyone guide me if in a wrong way I am or i missed anythong? [1]: https://www.biostars.org/p/342756

edgeR logfc

updated 3.6 years ago • H

div class="preformatted"> Hi, I have been trying to create a DGEList object in edgeR, using the following command: > tar<-read.delim("test_target.txt") > b<-readDGE(tar) Error in readDGE(tar) : Repeated...tags are unique using awk '{print$1}' | sort|uniq and yet I keep getting this error. I have used edgeR successfully in the past and am currently also able to us…

edgeR edgeR

updated 11.6 years ago • Guest User

div class="preformatted">Hi All, I am using edgeR for the DE analysis and in the user guide I noticed to use the following code: sum(p.adjust(de.common$table$p.value, method

edgeR edgeR

updated 13.6 years ago • Sridhara Gupta Kunjeti

Hi Naomi, Thanks for your interesting questions about the edgeR model. 1) We assume that variability in RNA-seq counts come from three sources: a) sampling variability associated with...Hi Naomi, Thanks for your interesting questions about the edgeR model. 1) We assume that variability in RNA-seq counts come from three sources: a) sampling variability associated with sequencing (for each …

Sequencing edgeR

updated 2.3 years ago • Gordon Smyth

<div class="preformatted"> Gordon K Smyth <smyth ...="" at=""> writes: > > 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 way. > > Total count filtering is not so bad, but it is sus…

miRNA edgeR miRNA edgeR

updated 10.3 years ago • Daniel

Running R ver. 3.4.0, after generating an error message with an edgeR load, I updated bioconductor and then re-installed, i.e. via biocLite("edgeR") library(edgeR) produced the following error...Error: package or namespace load failed for ‘edgeR’ in get(Info\[i, 1\], envir = env):  lazy-load database '/Users/adamfreedman/Library/R/3.4/library/edgeR/R/edgeR.rdb' is corrupt...In get(In…

edgeR package installation

updated 7.2 years ago • afreedman405

<div class="preformatted">Sorry to resurrect a somehow old thread, but I wanted to kick the tires on this and wanted to clarify the google-record for posterity ... so: On Sun, Jul 20, 2014 at 5:18 PM, Gordon K Smyth <smyth at="" wehi.edu.au=""> wrote: > > On Mon, 21 Jul 2014, Gordon K Smyth wrote: > >> logCPMc <- removeBatchEffect(y, batch) …

updated 10.1 years ago • Steve Lianoglou

all 36 possible combinations. I have count data for all cell lines. So whether I should analyze by edgeR or DeGseq? Can I perform exact test/GLM on this sort of data. I am very new to analyze this kind of data and I would appreciate

edgeR edgeR

updated 13.0 years ago • rakhs shit

I was reading blog posts, manuals and tutorials to find a good DEG pipeline. I thought edgeR was a good choice and tximport was good to summarise my transcript level abundances, but then I saw this tweet from a...I was reading blog posts, manuals and tutorials to find a good DEG pipeline. I thought edgeR was a good choice and tximport was good to summarise my transcript level abundances, bu…

tximport edgeR

updated 4.2 years ago • simon.michaelis88

Dear all, I am a edgeR user and I would like to know if edgeR reports 'average' cpm for each of the conditions tested in the analysis. Having a look

edgeR

updated 7.5 years ago • Anna Esteve Codina

div class="preformatted">Hi, We are examining the use of edgeR to analyze allele-specific count data from RNASeq experiments. In these studies, each biological replicate (n=18) has...bias. My question relates to how to best handle the normalization of the counts in this case. EdgeR applies calcNormFactors to the columns, which disrupts the maternal:paternal count ratio for each gene in eac…

RNASeq Normalization edgeR RNASeq Normalization edgeR

updated 10.3 years ago • Christopher T Gregg

with me. Regarding differential gene expression analysis from RNA-seq experiment, as far as I read, edgeR accept raw count and normalize with TMM method, is it right? However, I read in a paper used edgeR for differential expression...one of samples stands out from the rest, please let me know if we normal these data before running edgeR analysis?    Thank you in advance &…

edgeR differential expression normalization

updated 8.5 years ago • Sara

div class="preformatted"> I am new to R and edgeR. I am trying to follow to example 9. Case Study: deep-sequenced short tags from the edgeR manual. I download the data from

edgeR edgeR

updated 10.7 years ago • Guest User

gt; least 2 cpm in >= 10 samples, that may take care of the one-offs. >> >> Second, edgeR (unlike limma) doesn't have to ability to automatically adapt >> the degree of empirical Bayes smoothing, but you can...adjust it yourself. The >> default prior degrees of freedom for the edgeR empirical Bayes procedure is >> set a…

RNASeq GO edgeR RNASeq GO edgeR

updated 11.2 years ago • Simon Melov

div class="preformatted">Hi Gordon, I was looking in the devel code for edgeR and I noticed this new check in glmQLFTest: > if(!is.null(disptype)) if(disptype=="tagwise") stop("glmfit should be computed...same dispersions and such, due to this quote from the glmQLFTest help text in the current release of edgeR: > [glmQLFTest] behaves the same as ?glmLRT? except that it repla…

edgeR edgeR

updated 11.5 years ago • Ryan C. Thompson

Dear Mete, No, you cannot use non-integer counts with edgeR. If you must use non-integer counts, please use the voom() function in the limma package instead. This will do an analysis...that is not too different from edgeR, just a little less powerful, and is not bothered by non-integer values. Best wishes Gordon __Edit__: more recent versions...of edgeR do now allow non-integer counts. How…

edgeR

updated 5.8 years ago • Gordon Smyth

count matrix which element is the number of reads within gene region for each data set. I applied edgeR and DESeq methods for this comparison. For this case, 1. edgeR uses Poisson by setting common.disp=1e-6 (zero). 2. DESeq still...NB by assuming there is no difference b/w two samples to estimate dispersion. The results are 1. edgeR identifies many genes with very small p-values / adjusted p-…

edgeR DESeq edgeR DESeq

updated 13.2 years ago • Woo, Sangsoon

div class="preformatted"> Dear list, I am using EdgeR to calculate differentially expressed genes of RNAseq data. the toptags output gives me both a p-value and an FDR value

edgeR edgeR

updated 11.8 years ago • Kaat De Cremer

I have several questions about tximport results used for edgeR. According to the tximport vignette, the ideal method is to provide the estimated counts from the default condition...with an offset that corrects for changes to the average transcript length across samples for edgeR analysis. Your example of creating a DGEList for use with edgeR is as follows: <pre> library(edgeR) cts &…

tximport edger

updated 6.6 years ago • Xiang Wang

you mean by single nucleotide based normalization, however the following comments may be helpful. edgeR automatically adjusts for library sizes, whether you include an explicit normalization step or not. Normalization...is a separate issue, and is intended to deal with more subtle issues. Normalization, as edgeR does it, does not require replicates. Best wishes Gordon > Date: Fri, 04 …

Sequencing RNASeq Normalization edgeR Sequencing RNASeq Normalization edgeR

updated 13.6 years ago • Gordon Smyth

step. I would like use the total read count normalization method to normalize the data then use the edgeR to test my multi-factor models as in my previous post. The total read count normalization is given as X_ij/(N_j/mean(N))=X_ij...gt; To: bioconductor at r-project.org, mlinyzh at gmail.com > Subject: [BioC] EdgeR multi-factor testing questions > > > Dear Gordon, &…

Normalization edgeR Normalization edgeR

updated 10.6 years ago • Guest User

limmaWorkflow.html#normalising-gene-expression-distributions)[ easy as 1-2-3 with limma, Glimma and edgeR" ](https://www.bioconductor.org/packages/release/workflows/vignettes/RNAseq123/inst/doc/limmaWorkflow.html#normalising...to assess if using spike-ins for normalization would be informative I performed normalization with edgeR and limma-voom (quantile or spike-ins), boxplots:   [![N…

edger limma voom normalization limma

updated 5.8 years ago • Konstantinos Yeles

div class="preformatted">Dear Bioconductors, I'm trying to use edgeR to compute the differential expression from some RNA-Seq data, but it seems to be generating some odd results. I'm running...edgeR on data on about 6000 genes, across 5 experimental conditions. When I compute the differential expression for any two...of these conditions edgeR it is returning a 'nan' fold-change for about 15…

Normalization edgeR Normalization edgeR

updated 13.0 years ago • Nick Schurch

of TF. TFs were mapped using the CUT&RUN method. To do the differential analysis we used EdgeR and TMM normalization. However, in one case where there is more total level of TF in one condition compared to the other...to incorporate spike-in normalization. Does anyone know how to incorporate spike-in normalization to EdgeR differential analysis? Thank you

CUTandRUN edgeR Normalization SpikeIn ChIPSeq

updated 3.9 years ago • Hesh

Due to the increase in functionality in edgeR, I've become slightly confused about the correct order of calling the different functions, since there seems to be multiple...also has an argument called `` robust ``, which is suggested to be set to `` TRUE `` in the edgeR user guide. Is running `` estimateDisp(robust=TRUE) `` similar to running `` estimateGLMRobustDisp ``? </span> To…

edger estimatedispersions glm

updated 8.5 years ago • maltethodberg

div class="preformatted">Dear the edgeR community, Good day. 1. Could someone please light me, does the "topTags" show also the down-regulated genes/tags in the top

edgeR edgeR

updated 12.3 years ago • KJ Lim

div class="preformatted">Hi, We are working on a glm analysis in EdgeR and voom() and I am hoping we can help with our design. Currently, we are getting errors. We have 18 RNA-Seq biological replicates...and father B, and nine samples have mother B and father A. we wish to test the following models in edgeR and voom() (~sample+allele+parent) vs (~sample+allele) (~sample+allele+allele:pare…

edgeR edgeR

updated 12.2 years ago • Christopher T Gregg

div class="preformatted">Dear edgeR community, Good day. Please forgive me if I ask a stupid question. May I ask, using trended dispersion to estimate genewise

edgeR edgeR

updated 11.7 years ago • KJ Lim

i was trying to using trinity to do Differential Expression Analysis, which need to install the edgeR first.   After installing the package with two steps:  > source("http://bioconductor.org/biocLite.R") &nbsp...gt; biocLite('edgeR')   i got some error messages as following: BioC\_mirror: http://bioconductor.or…

edgeR limma

updated 8.1 years ago • zhongzaixuan

Dear Iddo, No, it is not valid to use a different design matrix for the dispersion estimation. edgeR will handle your model with 400 samples, but it will admitedly be slow. If this is too slow, then switch to voom() in the limma...package, which will be very fast, or to glmQLFTest() in the edgeR package, which will still be relatively slow but faster than the glm routines in edgeR (or DESeq2). …

limma edgeR DESeq2 limma edgeR DESeq2

updated 10.3 years ago • Gordon Smyth

at="" wehi.edu.au=""> >From: Jenny Drnevich <drnevich at="" illinois.edu=""> >Subject: edgeR with only 1 replicate? > >Hi Mark and others, > >Can edgeR be used if you only have 1 replicate per group? If not, do >you

Sequencing SAGE edgeR Sequencing SAGE edgeR

updated 15.2 years ago • Jenny Drnevich

<div class="preformatted"> Dear all, I am currently trying to use easyRNASeq in order to create a DGElist object for edgeR. However, when I run the function on my samples (as shown below), I encounter an error message AFTER counting: Preparing output...Dear all, I am currently trying to use easyRNASeq in order to create a DGElist object for edgeR. However, when I run the function on my s…

BSgenome BSgenome edgeR easyRNASeq BSgenome BSgenome edgeR easyRNASeq

updated 11.8 years ago • Guest User

div class="preformatted">Hello list, I'm trying to use read counts normalized with edgeR outside R. After a DGEList has been normalized by TMM and dispersion has been estimate (at least with estimateCommonDisp

edgeR edgeR

updated 11.6 years ago • Cittaro Davide

about either using normalized counts from EDASeq or raw counts with offset values of EDASeq in edgeR GLM for differential expression. I read edgeR manual where it says:</span> "The correction factors may take the form of scaling...sizes. Alternatively, gene-specific correction factors can be entered into the glm functions of edgeR as offsets." Also it is mentioned that estimateCo…

edgeR EDASeq

updated 9.1 years ago • rahilsethi

div class="preformatted">Hi All, I am working on sRNA-seq data and with no replicates and using edgeR to identify differentially expressed tags and using an arbitrary BCV value (0.3) based on suggestion in edgeR manual...replicates. " But I came across this post which mentions a conservative way to calculate BCV: [BioC] EdgeR: general advice on using edgeR for sRNA analysis: https://stat.eth…

edgeR edgeR

updated 10.8 years ago • Bade

div class="preformatted"> All, I am a new edgeR user. I have difficulty understanding the meaning of the ???cpm??? function of edgeR package. I mean I understand that each

edgeR edgeR

updated 11.6 years ago • Guest User

but has been troubling me for a while. How is fitting a negative binomial glm in R different from edgeR DE analysis. I think edgeR allows one to model a different variance for all genes, which is not feasible in the standard...glm.nb I can analyze all the samples together using drug and disease as two factors (0/1). However, edgeR only allows pairwise comparisons, such as between cases with no dr…

edgeR glm

updated 9.2 years ago • dongamit123

at="" dundee.ac.uk=""> > To: bioconductor at r-project.org > Subject: [BioC] Problems with edgeR for differential expression. > > Dear Bioconductors, > > I'm trying to use edgeR to compute the differential expression...two of > these conditions edgeR it is returning a 'nan' fold-change for about > 1500 out of the 6000 genes being tested. …

Normalization edgeR Normalization edgeR

updated 12.9 years ago • Gordon Smyth

Hello All, I have an RNA-seq dataset and I've performed PCA analysis to check batch effect using package edgeR. and have used raw counts from cuffnorm output. here is my code     library(edgeR)     a1<-read.table("raw\_counts.txt", sep="\\t", header=TRUE)     dge1 <- DGEList(counts=a1\[(-1)\]) …

rna-seq edger limma removebatcheffect()

updated 6.6 years ago • cvu

I'm unable to load edgeR even if it installs correctly. I'm new to this field so a lot of things might be naive. thank you in advance for any help! ``` Error...package or namespace load failed for ‘edgeR’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/Library/Frameworks/R.framework/Versions/4.2-arm64...Resources/library/edgeR/libs/edgeR.so': dlopen(/Library/Frameworks…

edgeR

updated 21 months ago • Vittorio

and abnormal. I utilized common dispersion, and the results are displayed at the end. When using edgeR, I have some questions as follows, 1) according to the results got from *summary(decideTestsDGE(de.com, p.value = 0.05))*, it...1 and 2 are not consistently greater than those in library 3 and 4. So I wondered how the package edgeR deals with this kind of inconsistent data. Is it still reliable…

miRNA edgeR miRNA edgeR

updated 13.0 years ago • Zhenling Peng

isn't a way to model a factorial experiment that is more powerful than the methods indicated in the edgeR User's Guide. The methods in the User's Guide already fully account for the fact that the double mutant has expression...gt; To: "bioconductor at r-project.org" <bioconductor at="" r-project.org=""> > Subject: [BioC] edgeR complex partial multifactorial design > > …

edgeR edgeR

updated 10.7 years ago • Gordon Smyth