Bioconductor Forum

Hi, I'm using DESeq2 to run analysis on 3 different cell types undergoing the same treatment conditions, each with 2 replicates (see metadata...are shared and unique between cell types. I've analyzed each cell type in their own separate DESeq2 object using both replicate+treatment and treatment designs. Overall, I see the best precision with a known set of...targets when using the native DESe…

DESeq2

updated 2.4 years ago • Hope

I've recently started using DESeq2. Unfortunately, I don't have raw counts data but have normalized counts. How can I analyse gene expression for already...normalized counts using DESeq2

DESeq2

updated 3.4 years ago • lizaaa

I'm running an analysis on RNA-seq data from TCGA & need help understanding the coefficients in DESeq2. Here is my code so far: <pre> library('DESeq2') cts <- read.csv(file='/Users/Corey/Desktop/DESeq2/Final_DESeq2/GeneName.csv

deseq2

updated 7.0 years ago • coyoung

Hi,  I have an experimental design where I have 2 factors (A: 4 levels, B: 2 levels). I'm interested to look at both factor effects and its interaction. I'm having troubles understanding...of the interaction A:B? reduced model as: A+A:B means that I'm looking at DE genes considering factor B? reduced model as: B+A:B means that I'm looking at DE genes considering factor A? Thanks! &a…

deseq2 multifactorial design reduced model

updated 8.9 years ago • laianavarromartin

gt; Hi, > > I´m a little puzzled about your 'Di erential analysis of count data { the > DESeq2 package' protocol. > > I was trying it with two samples and got the DE results, then I tried the > suggested transformations...would the formula be written in > that case? > cheers! if you have several conditions for one factor, we address this in…

Clustering GenomicRanges DESeq2 Clustering GenomicRanges DESeq2

updated 12.7 years ago • Michael Love

hi~ i meet an error when running ```r library("DESeq2") ``` the error message is: ```r error: package or namespace load failed for ‘DESeq2’ in dyn.load(file, DLLpath = DLLpath, ...): unable to...load shared object '/Users/zhengqimeng/Library/R/x86_64/4.3/library/DESeq2/libs/DESeq2.so': dlopen(/Users/zhengqimeng/Library/R/x86_64/4.3/library/DESeq2/libs/DESeq2.so, 0x0006): Library not loaded...…

DESeq2

updated 2.7 years ago • 启蒙

Please, could you help me. I have some doubts about the DESeq2 differential analysis.   We were performing a DEA analysis (report: <a href="http://rpubs.com/tiagochst/DESeq2...target="_blank">http://rpubs.com/tiagochst/DESeq2</a>) between some cell lines, and the gene log2FC for the ST13P12 gene caught our attention.   In the section …

deseq2

updated 7.6 years ago • Tiago Chedraoui Silva

Within the function `momentsDisEstimate()` of `DESeq2` a rough method-of-moments estimate of the mean counts is derived by this equation `(bv - xim*bm)/bm^2 `. (I am aware that this is...page. Thats why I formulated a question on: https://stats.stackexchange.com/questions/399685/deseq2-method-of-moments-negative-binomial `momentsDispEstimate <- function(object) { ` `xim &l…

deseq2 method-of-moments negative binomial

updated 6.8 years ago • Fischer-philipp

1. I am trying to add gene names to my result table from DESeq2 using the mapIds functions as outlined in the tutorial for differential analysis of RNA-seq data. However I get the...names to my table?   2. Is there a way to add the gene names to the dds generated using the DESeq2 function:  dds = DESeqDataSetFromHTSeqCount   thanks in advance for your time &nb…

deseq2

updated 10.3 years ago • mtsompana

Hello everyone, I need to do differential ChIP-Seq analysis to find the binding of genes between 2 conditions. I know there are lots of tools for that but I decided to use DESeq2 for that. I used MACS for peak calling and I had BAM files. Then used featureCounts to generate counts matrix. To this count...binding of genes between 2 conditions. I know there are lots of tools for that but I decided…

chipseq deseq2 featurecounts differential binding analysis

updated 7.6 years ago • hkarakurt

Is it possible to extract the baseMean data from each replicated sample using DESeq2? In DESeq, the output was arranged in a format of baseMeanA, baseMeanB, etc. that correlated with each sample. In DESeq2

deseq2

updated 11.1 years ago • aburkha69

if we could group samples with the same alleged condition. Given this scenario, I want to use DESeq2 to find out differentially expressed genes. The problem is: few biological replicates in the case group and possibly...I know that in edgeR one could 'fake' some parameters. Is there a way of doing the same in DESeq2?&nbsp

deseq2 rnaseq

updated 11.2 years ago • daniel.silvestre

Hey, Had something really strange happen to me when running my normal DESeq2 work flow. The counts function is giving the error message: Error in UseMethod("counts") : no applicable method for 'counts...This even occurs when I run the example from https://www.rdocumentation.org/packages/DESeq2/versions/1.12.3/topics/counts Input: dds <- makeExampleDESeqDataSet(m=4) …

deseq2 Deseq RNAseq

updated 6.1 years ago • mrfossl97

Hello, I have RNAseq data from a longitudinal study, where six participants provided samples first at 0 dose, then at a low dose (25) of medication, and then at a high dose (35) of the same medication.  There are no massive...Hello, I have RNAseq data from a longitudinal study, where six participants provided samples first at 0 dose, then at a low dose (25) of medication, and then at a…

deseq2 multiple time points dose

updated 8.9 years ago • stwestreich

s still a little bit tricky to explain the results back to a scientist.  The dispersion, size factors, and more importantly betaPriorVars, were all estimated on a full dataset (which still exhibits the phenomenon), but...here I'm just reproducing a few rows. <pre> set.seed(1) library(DESeq2) myCounts <- t(matrix(c( 280, 183, 232, 205, 245, 149, 184, 186, 164, 187, 289…

deseq2 differential gene expression

updated 9.4 years ago • Gavin Kelly

I'm trying to use DESeq2 with glmGamPoi as a fit type for scRNAseq data. If I run: ``` deg <- DESeq(dds, fitType="glmGamPoi") ``` I get a warning that `glmGamPoi...glmGamPoi", test = 'LRT', reduced = ~ orig.ident) ``` I get an error: ``` estimating size factors estimating dispersions gene-wise dispersion estimates using 'glmGamPoi' as fitType. If used in published…

DESeq2 glmGamPoi scRNAseq

updated 4.8 years ago • tatyana.perlova

div class="preformatted">Dear all, I want to locate transcription factor binding sites (tfbs) within a given sequence. The tfbs are derived from databases like transfac or jaspar and are described

Transcription Transcription

updated 17.7 years ago • Hans-Ulrich Klein

ignore empty levels. x = Rle(c(2,3,1,2,3,2),rep(2,6)) levels(x) = as.character(0:5) table(x) table(factor(as.numeric(x),levels=as.character(0:5))) I am using R 2.15.1 and IRanges 1.17.1. Regards, Pete ____________________ Peter

IRanges IRanges

updated 13.2 years ago • Peter Haverty

surprisingly) all signal after multi-hypothesis corrections. 4. Calculation of the DESeq2 adjusted p value (p_adj) - same as question #3, is the DESeq2 model appropriate for TnSeq data. We've noted that our RNAseq...datasets often have comparisons where one condition goes to 0 reads, and have read that the DESeq2 model can handle these conditions, though in the TnSeq dataset the n…

DESeq2

updated 8 months ago • Lynn

As described previously here: https://support.bioconductor.org/p/66067/ The way to access the normalized count table in DESeq2 can be done by the following script lines: dds <- estimateSizeFactors(dds) counts(dds, normalized=TRUE) I'm trying to understand if the normalized count table that can extracted using the above is taking into consideration a batch effect that is modeled in …

deseq2 edger normalization

updated 6.1 years ago • Matan G.

Dear All! I have the following setup for an RNA-seq experiment: 4 individuals, 2 of them have a disease, 2 are healthy controls, cells from each individual were cultured using two different conditions. So, the setup is very similar to the one described in the edgeR user guide (Section 3.5) or in the DESeq2 vignette (Section 3.12.1). Following the edgeR user guide I generated the design matrix (`…

edger deseq2 rna-seq

updated 10.5 years ago • Johannes Rainer

Hi all, I am currently exploring normalization strategies such as EDASeq [ref; https://doi.org/10.1186/1471-2105-12-480] to address technical artifacts like GC-content and to account for both within- and between-lane normalization. As illustrated in the EDASeq vignette, such normalization factors can be readily incorporated into the edgeR framework through the "offset" slot. This function…

deseq2 EDASeq

updated 6.4 years ago • jeroen.gilis

I tried to run DESeq2 and the following error occurred when I'm installing the same. The version of R I use is R 4.3 and the DESeq2 version is

DESeq2

updated 2.7 years ago • rajarajeshwari

Hi all, I would like to use DESeq2 for my DE analysis. I have a quite big dataset of about 200 samples, divided into 16 treatments. For each treatment, I have...to perform a batch correction, and for this reason, I would not be able to use raw data as input for DESeq2. Do you have any suggestions on packages that will still allow me to use it or if there is a way to correct my data with…

DESeq2

updated 4.8 years ago • Alessia

HI, Michael, I read your DESeq2 vignette: http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html and found that DESeqDataSet...matrix. I wonder if you ever compare the results of these two process (salmon->tximport->DESeq2 versus counts->DESeq2) for differential gene call from the same sequencing dataset? Thanks. C

DESeq2

updated 7.0 years ago • capricygcapricyg

the counts of peak. if using the DESEQ method, diffbind will make analysis. so, can I directly use Deseq2 to analyze the consensus peak set. there are more other packages can analysis with Deseq2

deseq2 diffbind

updated 5.4 years ago • qq809825706

sequencing platforms used, illuminaHiseq and IlluminaGA. Is there a way to remove batch effects in DESeq2 package prior to differential expression or does the GLM remove it automatically (which i dont hink happens). Thanks

deseq2 batch

updated 6.8 years ago • sherajilir

Dear all, I ran a DESEQ2 script to evaluate gene ratio changes. When I have a look on the raw data it seems that the ratio is higher in the PET14...diagdds = phyloseq_to_deseq2(psPE_T14, ~ Polymer) calculate geometric means prior to estimate size factors gm_mean = function(x, na.rm=TRUE){ exp(sum(log(x[x > 0]), na.rm=na.rm) / length(x)) } geoMeans = apply(counts(diagdds), 1, gm_mean) di…

phyloseq DESeq2

updated 3.6 years ago • Stephan

Dear all, Briefly, I’m developing a tool to perform network analysis on an interactome weighted by RNA-seq counts. Even if I also did a differential expression analysis to get the list of DE genes, my topic here is related to the generation of normalized/transformed counts in order to weight the nodes of the interactome. This weight will be then used to analyze the network. I would like to …

normalization CQN deseq2 RNA-seq network

updated 6.6 years ago • michael.pierrelee

After reading some post that recommend checking p-value distributions after DE testing, I went back and looked at some data where the result of DE testing was 0 significantly DE genes (3 replicates, 3 conditions, 3 times). Note that this was using an experiment where all samples were loaded into DESeq2 so that additional samples could be used for dispersion estimation. It turns out those p-value …

deseq2 rnaseq fdrtool dispersion

updated 8.2 years ago • rrcutler

I'm trying to figure out how to interpret a model design with 3 factors plus interactions. I have young and old mice, untreated and treated, in two timepoints. I'm interested to see the treatment...s8 old treated 3 ``` I am treating it as a time-series analysis, with 3 categorical factors plus interactions. ``` dds <- DESeqDataSetFromTximport(all.txi.kallisto, sample.s…

deseq2

updated 5.9 years ago • demisa

within one hour - ask someone!" So here I write, my question regarding model matrices in limma or DESeq2. I will copy a reprex first: ``` r # Create data frame with information. groups <- data.frame(group = c(rep(1,6), rep(2,6), rep(3,6), rep(4...c(rep(c(1,2,3), 4), rep(c(1,4,5), 4))) # Setting levels for fixed effects. groups$treatment <- factor(groups$treatment) gr…

limma deseq2

updated 6.5 years ago • Ben

Hi, I'm trying to run DEseq2. As a test I'm using RNAseq data from 8 samples.  My countdata, coldata, and rowdata objects look (to me) formatted as...Hi, I'm trying to run DEseq2. As a test I'm using RNAseq data from 8 samples.  My countdata, coldata, and rowdata objects look (to me) formatted as they...rownames were renamed by adding numbers</pre>   _Here is th…

DESeqDataSet DESeqDataSetFromMatrix rnaseq deseq2

updated 9.5 years ago • ErickF

across four growth conditions: "BHI", "SCFM2", "AZM", and "TOB". I have provided the output of the first 10 rows of the raw counts obtained using featurecounts below. I have also provided the metadata table I used for the...1 SCFM2_TOB_2 TOB Antibiotic 2 ``` The problem I'm having is that DESeq2 was able to identify 1000+ differentially expressed genes between SCFM2 and AZT or…

DESeq2

updated 4.6 years ago • Naphtap92

I'd like to perform an experimental design for DESeq2 package using the LRT Test. I've already done it before using two different conditions Treated (T) vs Untreated (U), each...time point 0 and T replicated samples at different time-points. Is it possible to perform it with DESeq2? I'm not able to find examples as in this special case, but i'm able to find several time-course data designed in …

rnaseq deseq2 time-course

updated 8.4 years ago • inzirio

to the latest version of R (3.2.0) and am still having trouble. I am trying to install and use DESeq2. Please see the below output and errors. Any help would be greatly appreciated! Thanks, Claire   R version 3.2.0 (2015...for Statistical Computing Platform: x86\_64-apple-darwin13.4.0 (64-bit) \#error upon installing DESeq2 > biocLite('DESeq2') BioC\_mirror: http://bioc…

deseq2 r software error

updated 10.7 years ago • rclaire

I have been using your MotifDB software. I am curious how many unique transcription factors are in your updated database. Thank you for your time

motifdb

updated 8.2 years ago • scotronq

Hi, My experimental design is as follows: 1 factor with 4 levels and want to consider batch effects. My approach is to considerate the design as ( full= ~ Batch + Condition...nbsp;reduced = ~ Batch ) the MA-plot appears with unshrunken results. plotMA(dds1, main= "DESeq2", ylim = c(-2,2)) However if I do apply betaPrior TRUE: dds2 <- DESeq(dds, test="LRT", b…

deseq2 LRT betaprior

updated 9.3 years ago • laianavarromartin

When using DESeq2, I noticed that some of my top genes have a pvalue or padj of zero. I suppose the pvalue from the Wald test is really small...When using DESeq2, I noticed that some of my top genes have a pvalue or padj of zero. I suppose the pvalue from the Wald test is really small and it got rounded at some point when I run DESeq2, although it is a bit surprising that other packages, includin…

deseq2 pvalue visualization enhancedvolcano rnaseq

updated 6.9 years ago • ricardo3889

Hi everybody, I'm using DESeq2 through phyloseq to identify bacterial OTUs that are significantly differently present between treatments. Yesterday...for certain which update is responsible. Old versions: RStudio 0.99.891, R 3.2.3, Phyloseq 1.14.0, DESeq2 1.10.1 : resulted in 65 OTUs significantly different between treatments New versions: RStudio 0.99.891, R 3.1.3, Phyloseq...1.16.2, DESeq2…

deseq2 phyloseq

updated 9.6 years ago • am39

I want to use deseq2 for differential abundance analysis for 16s amplicon data analysis. data detail: I do have three tissue: summary(sample_data

deseq2

updated 6.8 years ago • nabiyogesh

of FoldChange in this way?   2. If so can I generate them for FoldChange either in DESeq or DESeq2 with an R command?  I do have lfcSE from DESeq2 but 2^lfcSE does not seem to make sense, is there a way to generate? &nbsp...3. Can I get baseMeanA and baseMean B from DESeq2 or would that be identical to the DESeq1 output? Thanks, Lisa   &nbsp

rnaseq deseq2 deseq standard error confidence interval

updated 9.7 years ago • lisa.crossman

Hi, I have some output from DESeq2 to be processed by ReportingTools. In thread https://support.bioconductor.org/p/115810/#115817 it turned out it is...Hi, I have some output from DESeq2 to be processed by ReportingTools. In thread https://support.bioconductor.org/p/115810/#115817 it turned out it is a...title = "Results of differential expression analysis using DESeq2 (cancer vs. normal)",…

reportingtools

updated 7.1 years ago • mmokrejs

up a pipeline for RNAseq data analysis to identify differentially expressed genes (DEG) using DESeq2. I am trying to validate the results of my pipeline with previously published experiments but I dont seem to find any...papers using the current version of DESeq2 (v1.30.0) with available reads. I found that installing previous versions of DESeq2 can be troublesome and that different...results. …

DESeq2

updated 5.0 years ago • Samuel Daniel

Dear all,  I am trying to analyze my smallRNAseq data with Deseq2 and to run ReportingTools on it. I have different treatments and timepoints, I saw that you have a coef option to tell...possible to get all pairwise comparisons from the data set as log2FC, or to input the results from Deseq2 into those columns and keep the barplots. I tried to do them first as pairwise comparisons, bu…

R reportingtools deseq2 pvalue coef

updated 9.6 years ago • NMostajo

I have a direct question about DESeq2's memory handling. I have come to really enjoy DESeq2 for ATAC-Seq and it is really well documented etc. The problem is

deseq2

updated 8.2 years ago • Jeff Granja

Hi all,  I am new to R. I am trying install DESeq2 in R for RNA-Seq data analysis. But i am getting this error at the end..... 1: In install.packages(pkgs = doing, lib = lib, ...) :   installation...status 5: In install.packages(pkgs = doing, lib = lib, ...) :   installation of package ‘DESeq2’ had non-zero exit status I am working in Ubuntu 16.04 . Can anyo…

software error R deseq2 rnaseq

updated 7.8 years ago • k.kathirvel93

Your experiment has three genotypes and one treatment (stress vs control). When we analyse a two factor study, the first question we have to consider is whether it makes sense to assume that the treatment effect will be the...study, however, your non-treatment factor is genotype. Usually one would design a study of this type to see whether the treatment effect differs between genotypes...project…

edgeR edgeR

updated 13.8 years ago • Gordon Smyth

I try to install DESeq2 using bellow code in R 1.4.1717 BiocManager::install("DESeq2") Got this error Warning message: package(s) not installed...when version(s) same as current; use `force = TRUE` to re-install: 'DESeq2

DESeq2 Problem installation with

updated 4.5 years ago • Nahid

I have a complex time-series RNA-seq expression dataset which I'm currently trying to analyse using DESeq2. I have two plant species, grown under two nitrate levels along six days of a heat wave experiment (a day before the heat...the two species. Am I missing something here? I also tried to combine the species and nitrate factors to one species\_nitrate factor, and running the test wi…

deseq2

updated 9.3 years ago • giltu1

all, I was asked to repeat RNAseq analysis done a while ago. Previously, analysis was done using Deseq2 v1.2.10 and R v.3.0.2. Although we are still using the same version for Deseq2, R on our system is now upgraded to 3.2.1

deseq2

updated 10.2 years ago • genomica

like to block for center. I.e. the center is like a batch effect. Is it possible to block for two factors, suject and center, in the same test in Limma? /Ingrid -- output of sessionInfo(): See section 8.7 in the user guide. -- Sent via

limma limma

updated 12.6 years ago • Guest User

First time RNA-seq analyst here. I'm new to the ONT MinION platform, but not to R. I was wondering if anyone had experience using...DESeq2 to analyze the long read, direct RNA sequencing results generated by the MinION. I have attempted to use minimap2 to...that are specific to noisy long reads) , resulting in SAM/BAM files. I want to take them into DESeq2, which is favored by my colleagues. Howe…

deseq2

updated 6.6 years ago • uhlkatie

Hi, I am using DEseq2 to perform differential analysis of control and treated samples. However, I am not sure if DEseq takes into account...of the reads are aligned, the greater the numReads is, does this get taken into account in DEseq2 or do I need to account for it myself before DEseq2? Thank you, Dan

deseq2 salmon rna seq salmon

updated 7.1 years ago • danalvoronov

div class="preformatted"> Hi there, I am currently making multiple comparisons using contrast in DESeq2. I am interested in differential expression for genes underlying germination mechanism due to high temperature...Dec 23rd, 2013, page 11). I understand the terms 'condition', 'factor level', and 'group' are being used vaguely for flexibility purpose. I just want to make sure I am interpreti…

DESeq2 DESeq2

updated 12.0 years ago • Guest User

Hi all, I want to run sva and include the results in the design passed to deseq2 looking for degs. Sva takes normailzed counts, but deseq2 takes raw counts and normalises also. So if I proceed, the data...it ok to normalize twice? Should I remove surrogate variables and de-normalize before passing to deseq2? Should i run deseq2 but prevent it normalizing again? I realise sva is…

DESeq2 Normalisation Bulkrnaseq Svaseq

updated 19 months ago • BioinfGuru

you so much for the platform and as usual, I may have your few minutes to my question? I used both DESeq2 and edgeR to analyze my RNAseq data. However, I found a higher number of significant genes in my DESeq2 analysis compared...fit, design = design) table(p.adjust(QL$table$PValue, method="BH")<0.05) #### 5928 genes ``` ``` ### DESeq2 dds <- DESeqDataSetFromMatrix(countDat…

deseq2 edgeR

updated 5.7 years ago • Do it!

expression between two groups of 10 and 6 samples. After reading several posts about the use of DESeq2 on NanoString data, and following the tutorials and code provided in the GitHub linked in the publication [An approach...of these so called housekeeping genes and the phenotype. Following the pipeline, I estimated RUVg factors (using all of the 40 housekeeping genes) and used the following…

NanoNormIter DifferentialExpression Housekeeping DESeq2 NanoString

updated 4.0 years ago • argonvibio

Can we use deseq2 for 16s metagenome analysis? If yes is there any specific pipeline for it? &nbsp

deseq2

updated 8.4 years ago • saiprabhask4

I just updated R, RStudio and Bioconductor (sessionInfo at the end). I reinstalled DESeq2 with no error messages. But I cannot load it. Thanks. library(DESeq2) Error: package or namespace load failed for ‘DESeq2...I just updated R, RStudio and Bioconductor (sessionInfo at the end). I reinstalled DESeq2 with no error messages. But I cannot load it. Thanks. library(DESeq2) E…

DESeq2 load

updated 2.8 years ago • Naomi