Bioconductor Forum

I have situation pretty similar to <a href="https://support.bioconductor.org/p/95493/#95570" id="DESeq2 likelihood ratio test (LRT) design - 2 genotypes, 4 time points" name="DESeq2 likelihood ratio test (LRT) design - 2 genotypes...for point 1) As explained in the linked post and the vignette i can use <pre> dds$group <- factor(paste0(dds$line, dds$day))</pre> …

deseq2

updated 7.9 years ago • Matteo Perino

nbsp; Hi, I'm running the DESeq function in DESeq2 as follows:   ddsRep = DESeqDataSetFromMatrix(countData=countData,                 &nbsp

deseq2 averagePriorsOverLevels

updated 9.5 years ago • laianavarromartin

My question is if any of you have experience with QuantSeq data and know if it's possible to use DESeq2 directly in the data produced? Thanks in advance

deseq2

updated 6.8 years ago • andrebolerbarros

Hi! I'd like to use the deseq2 rlog transformation in order to use the normalized matrix for pca and heatplots. I understood that I should use the

deseq2 normalization

updated 11.1 years ago • francesca.defilippis

Hi everyone, I am using DESeq2 to analyze my RNAseq data and really like the package. There is lots of information available, a very helping community

deseq2 normalization normalized counts

updated 7.8 years ago • naets_matthias

Hello, My aim is to use a (kallisto|salmon)/tximport/DESeq2 pipeline using length-corrected gene count estimates. The tximport vignette provides two methods for importing...matrix txi$counts directly as you would a regular > count matrix with these software" For DESeq2, I took this to mean taking txi$counts and then passing this object as the first argument to `DESeqDataSetFromM…

tximport deseq2

updated 6.9 years ago • Thomas Bradley

I am trying to do `DESeq2` on the dataset [GSE202203][1]. I downloaded the data from the server using [GSE202203_RawCounts_gene_3207][2] link. But...was in fraction number as follows: ![df][3] How do I effectively convert the values compatible for DESeq2 analysis? Is this way correct? `df[,-1] <-round(df[,-1],0)` [1]: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE202203 [2]:…

DESeq2 TPM rawcounts StringTie

updated 3.4 years ago • snijesh

Hi, I am running a DESeq2 analysis for some data. I have two different conditions in my data which should have identical RNA-seq at day 0 (I am doing...a time course experiment). However, when I run them through DESeq2, I get a hill-shaped pvalue distribution (plotting non-adjusted p-values), shown below. Do you have any idea why this might

DESeq2

updated 2.8 years ago • gdolsten

from both ribosome profiling (Ribo-seq) and RNA sequencing (RNA-seq) data. I'm considering using DESeq2 to analyze differential expression of these TE values between the conditions to identify genes with significant...counts for each gene, I would appreciate your advice on the best approach for this analysis using DESeq2. Specifically, I would like to understand: 1. How should I structure the …

RiboSeq DESeq2

updated 16 months ago • noi.cohen

Hi all! I am analyzing RNA-seq data with DESeq2, and I have two confounding variables. One is the batch number and the other is whether cells were washed or not. The data...Hi all! I am analyzing RNA-seq data with DESeq2, and I have two confounding variables. One is the batch number and the other is whether cells were washed or not. The data is comprised of samples of two different ce…

deseq2 design matrix multi-confounders linear models rna-seq

updated 5.9 years ago • mohamedrefaat.1.1992

is not an integer, btw, is it ok?) And i'm having a bad time adjusting my data to right format for deseq2 package.  Can i mb see an actual format for input data, so i would create such a file by python script?&nbsp

deseq2 R RSEM

updated 8.0 years ago • tim.ivanov.92

that we use the tximport to get gene level read counts and gene length. Now we are trying to use DESeq2 to do differential expression analysis and we want to include the gene length for correction between species. But...to set "tx2gene" to two different species. Below is briefly our codes. Is this correct and DESeq2 will use the gene length when do differential analysis? #const…

deseq2 Kallisto tximport

updated 6.6 years ago • qwzhang0601

Hi, I used DESeq2 to analyze RNA-Seq data, and obtained some results that are hard to explain. Could anyone help me? Please see the...Hi, I used DESeq2 to analyze RNA-Seq data, and obtained some results that are hard to explain. Could anyone help me? Please see the following...figure is MA plot which shows the result of differentially expressed genes identification us…

deseq2

updated 8.0 years ago • jQ

nbsp; From the DESeq2 vignette: <pre> txi <- <strong>tximport</strong>(files, type="salmon", tx2gene=tx2gene) ddsTxi <- DESeqDataSetFromTximport...Q1. Is it possible to normalise a gene expression matrix (produced by Salmon and tximport) using DESeq2 method without sample information? The goal here is to obtain a DESeq normalised expression matrix. Q2. As a…

deseq2

updated 7.6 years ago • user31888

Hello, I am encountering a fully reproducible failure when running DESeq2 in parallel using MulticoreParam on macOS (ARM). The error appears to originate inside BiocParallel and occurs even...the full traceback, and my sessionInfo(). --- ## Minimal reproducible example ```r library(DESeq2) library(BiocParallel) set.seed(1) dds <- makeExampleDESeqDataSet(n=1000, m=6) dds <- DESeq…

BiocParallel DESeq2

updated 5 weeks ago • Benjamin

My question is quite simple, I want to know is it possible to use TPM data to normalize them with DESeq2? and why

counts Normalization DESeq2

updated 3.7 years ago • Hicham

Currently, the only way to use `altHypothesis` in DESeq2 is through `results`. However, this doesn't allow to use `altHypothesis` in shrunken LFC values. I want to isolate genes...Currently, the only way to use `altHypothesis` in DESeq2 is through `results`. However, this doesn't allow to use `altHypothesis` in shrunken LFC values. I want to isolate genes with

deseq2

updated 6.5 years ago • zefrieira

Dear community, I have an RNA-seq project with three factors: A, B and C, where A and B are random effects, while C is fixed effect. As I know, DESeq2 and edgeR cannot take care of the random

rna-seq

updated 9.6 years ago • Yanzhu Lin

Hello, I am using DESeq2 to analyze ATAC-seq data. The samples are from human patients, pre and post therapy -- so, require a paired analysis which...Does the order matter? I don't think I can remove the batch effects with Limma or Combat prior to DESeq2 because it requires raw counts as input. Any advice would be greatly appreciated! Thank you! Josephine

deseq2

updated 8.8 years ago • jogiles

Hi, I'm analysing RNA-seq data in `DESeq2`. To make sure if data is loaded properly I compared count plot from `ggplot` and plot from exported values after accounting...for size factor (I used the product of count and size-factor). Plot from exported values was done in libreoffice. The plots is slightly

DESeq2 ggplot2

updated 19 months ago • boczniak767

I have a SingleCellExperiment object, and no matter what I do, when I run `normalize(filtered.sce)`, I get the error: `size factors should be positive real numbers`. It is my understanding that even though `computeSumFactors()` coerces to positive by default if necessary, it doesn't imply that `normalize()` will run automatically. I have done many things to my pancreas dataset (Segerstolpe…

scater scran singlecellexperiment normalize qc

updated 6.7 years ago • kushshah

24h,13C,anoestrous,anoestrous_24h sample_54.bam,48h,13C,anoestrous,anoestrous_48h</pre>   At first I did not have the last column (phaseANDtimepoint) but I had to add since I want to retrieve the following comparisons...lt;- read.csv("exp2_metadata.csv") colData(se_exp2) <- DataFrame(sampleTableExp2) library(DESeq2)</pre> at first, I have done: <pre> dds_…

deseq2 rna-seq interactions contrast

updated 7.3 years ago • Maithê Barros

Hi, I have a 2 factor experiment (2 mutations:A,B), with 2 levels (+/-) in each factor. All together there 4 conditions: wt, A, B, and A+B , with two replicates

deseq2 LRT

updated 5.4 years ago • guyho

all, I have the experiment with the design like this: [design][1] ---------- When I used the DESeq2, I used the code: dds <- DESeqDataSetFromMatrix(countData=countdata, colData=coldata, design=~condition + batch) to remove

deseq2

updated 5.8 years ago • luongthang1908

Hello, I use the DESeq2 package for many projects in which the number of samples is quite small. But, sometimes i have some projects with almost

deseq2

updated 8.2 years ago • stevenn.volant

div class="preformatted"> Hi all, I have entered dependency hell when trying to install DESEq2. I am using Rstudio that is running on linux Mint, with R version 3.0.1. When I run biocLite(c("DESeq2"), dependencies = TRUE...what almost seems like a successful install (See below). I don't think this problem is specific to DESeq2, but does anybody have an idea as to what is going on here. Wa…

DESeq2 DESeq2

updated 12.4 years ago • Guest User

Why does setting lfcThreshold > 0 in `lfcShrink()` of DESeq2 report s-values instead of p-values when using apeglm shrinkage? Currently using Bioconductor 3.10, DESeq2 1.26.0

deseq2 apeglm

updated 5.5 years ago • jabaron.phd

Hello, I have some questions concerning the construction of design matrices within the DESeq2 package.\\\\ I constructed the following design matrix, which contains 3 different treatments (T1,T2,T3) in duplicates...pre>   I know that it is easily possible to convert it into a "colData" data frame, which DESeq2 "understands".: <pre> colData <- mat.or.vec(nrow(des…

deseq2 design matrix limma design matrix

updated 10.7 years ago • taf

Hello, I'm trying to perform one group vs multi group comparison with DESeq2. I have 17 groups. What I'm doing typically is following (suggestions followed from this post: [__DESeq2: one condition...Hello, I'm trying to perform one group vs multi group comparison with DESeq2. I have 17 groups. What I'm doing typically is following (suggestions followed from this post: [__DESeq2: one condition v…

deseq2

updated 7.8 years ago • v.t

Hi, I noticed in the DESEQ2 tutorial (https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html\#data-quality-assessment

deseq2

updated 7.7 years ago • owen.whitley

between control vs disease. Here is my knowledge on this: "Browsing through different sources on Deseq2, I can understand one can do this with linear modelling, and putting the variable of interest at the last of the model...my questions: 1. Will DiffBind work like that? I remember from the Vignette, about using Blocking factors, but it seemed to be not exactly as Deseq2 format, code wise. 2.…

DiffBind Deseq2

updated 5.2 years ago • bioinfouser2

to clarify what my understanding is as well as address a couple of questions. I have read both the DESeq2 and DDS papers that talk about dispersion shrinkage.    My understanding: The point of dispersion shrinkage...for this? 2) It is recommended for most cases to include all samples in the experiment when running DESeq2 in order to more accurately estimate the dispersion pa…

deseq2 DDS

updated 8.3 years ago • rrcutler

where multiple tumour regions per patient were sequenced (average 4/patient) and we are using DESeq2 to compare the transcriptomes of treatment responders vs non-responders: 1. In one comparison, we compared 31 regions...of DEGs with 'only' 259 DEGs Could the fact that the second comparison is less balanced than the first one at least contribute to such a drop (especially knowing that the …

deseq2 cancer

updated 5.3 years ago • bioconductor_user_1675

mapped reads for condition A was about 10% of that for condition B. I wonder if I can still run DESeq2 for differential analysis between A and B. Thanks a lot! C

deseq2

updated 6.5 years ago • capricygcapricyg

Hi all, I want to do meta-analysis with p-value of DESeq2,as you know there are some NA value for p-value in each experiment. what should I do with them,I can not remove them in each

deseq2 meta-analysis metaseq

updated 8.5 years ago • ed_isfahani

the count data for each gene using Kallisto. Can I use the count table from Kallisto as an input for DESeq2 to get the normalized counts?  Thanks, Yong &nbsp

rnaseq deseq2 kallisto

updated 9.3 years ago • yjliu1127

at the University of Virginia and new to RStudio. I am in need of assistance regarding my DESeq2 analysis. I would like to use DESeq2 to process paired RNASeq samples. I have over 100 samples from male and females patients...For each patient, I have two treatments (With-FBS and Without-FBS). I would like to run DESeq2 to identify the differentially expressed genes between males and females irresp…

DESeq2

updated 4.8 years ago • Rita

I have several gtf-files and a gff3 file representing different sets of genes. I want to count the expression using HTSeq-count and input them all to DESeq2. But I am not sure what is the best approach. I was thinking that I could simply concatenate all the gtf and gff3 files, but...different sets of genes. I want to count the expression using HTSeq-count and input them all to DESeq2. But I am no…

htseqtools deseq2 counts cuffdiff

updated 9.9 years ago • Jon Bråte

Hi, All I am new to Rstudio , i Have to study expression data for the following But my DESeq2 data is having an error of Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method...Hi, All I am new to Rstudio , i Have to study expression data for the following But my DESeq2 data is having an error of Error in h(simpleError(msg, call)) : error in evaluatin…

DESeq2

updated 4.1 years ago • mithu18mohan

I am learning about using ReportingTools for DESeqDataSet. Using the example in the [user guide][1]: ``` library(DESeq2) library(ReportingTools) data(mockRnaSeqData) conditions <- c(rep("case",3), rep("control", 3)) mockRna.dse <- DESeqDataSetFromMatrix(countData = mockRnaSeqData, colData = as.data.frame(conditions), …

ReportingTools

updated 6.8 years ago • psutton

Hi, I've been asked to do a Differentially expressed genes analysis using RNA-Seq from TCGA database. I've been using DESeq2 for all my previous analysis on cell lines. I'm having an issue with the control samples selection in TCGA. I've seen that DESeq2() should not be used with a mix of paired and unpaired tumors and controls dataset and that limma-voom duplicateCorrelation() should be u…

RNASeq DifferentialExpression DESeq2 tcga

updated 4.0 years ago • IamFrofro

I am using 2 different model specifications and I do not know if one of them is correct. a) A first solution is simply to include in the model the *day effect* as an additional fixed effect. I will assume that there is not...and *treatment effect*, so my design matrix will be of the form: design=model.matrix(~ - 1 + factor(treatment) + factor(day) ) fit=lmFit(eset,design) b) My ques…

limma limma

updated 19.5 years ago • Pedro López Romero

zebrafish RNAseq using STAR to determine abundances and we can successfully run this data through DEseq2. We would like to know whether it is possible to export a table/matrix from DEseq2 that shows the effects of the dispersion...corrections on the original input data (i.e. pre vs post DEseq2 effects on the actual abundance values). Thank you

DESeq2

updated 4.4 years ago • michael.morash

to mimic the experimental setup as follows: ```r sampleTable <- data.frame( Condition = factor(rep(c("Veh", "A", "AB"),each=9)), Time = factor(rep(c("1 day", "3 days", "7 days"), each = 3,time=3)) ) rownames(sampleTable) <- colnames(txi$counts) design

RNASeq DESeq2

updated 13 months ago • pm_25

Hi, I'm currently trying to assess fold change when comparing two different sample types using DESeq2 package and I'm getting weird Cook's distance values which are causing major problems. The two different samples have...Hi, I'm currently trying to assess fold change when comparing two different sample types using DESeq2 package and I'm getting weird Cook's distance values which are causing maj…

DESeq2

updated 2.9 years ago • miketomas89

Hi all, I'm doing RNAseq analysis with DESeq2. When making MA plot, I want to position each gene on the x-axis using its mean abundance from one condition

TPM deseq2

updated 7.2 years ago • georgewwp

Hi, I would to have a data frame with normalized counts of my RNA-seq data set. I used DESeq2 to analyse these data. This is the code I used to generate normalized counts : <pre> ddsHTSeq <- DESeqDataSetFromHTSeqCount

rnaseq deseq2 normalized counts

updated 7.6 years ago • JoannaF

I need to use DESeq2 in R so I tried installing it and it does not work. I looked online and it seemed to be a problem with XML so i tried to install

deseq2 libxml xml

updated 4.6 years ago • Fátima

Hi wondering how I can use the following DESeq2 logic within the framework of DiffBind for calling differential peaks and looking at multiple interactions: <pre

diffbind deseq2 interactions

updated 5.0 years ago • rbronste

Hi everyone I need to run Deseq2, but when I try to run this part of command the following error message appears. **Error in DESeqDataSet(se, design = design...ignoreRank) : 1 duplicate rownames were renamed by adding numbers** I am new to R and DESeq2, Please anyone could hepl me to fix this error. Thank you very much

DESeq2

updated 4.3 years ago • Abdou-samad

like to know the difference between p value and p adjusted value which is given an an output by Deseq2 package MY second question is what is the cut off of padj which would be ideal to determine deferentially expressed

deseq2 RNASeq padjusted

updated 6.9 years ago • tanyabioinfo

Dear All, I would like to plot residuals vs. fitted values for some of the candidate genes, after fitting the model and testing with DESeq2 package. Can someone tell me how I could extract the computed residuals and the fitted values per gene? Thank you in advance...vs. fitted values for some of the candidate genes, after fitting the model and testing with DESeq2 package. Can someone tell me how…

deseq2

updated 8.9 years ago • Mike Miller

RNA-seq data from several conditions where I have deteremined differentially expressed genes using DESeq2 and I'd now like to perform gene set enrichment analysis on the log2FC values from these comparisons. My question is

deseq2 gsea rnaseq gene espression

updated 6.9 years ago • bmreilly

Different number of DE genes using edgeR and DESEQ2 Good morning to everyone, I'm trying to compare the DE transcripts results obtained by using two different workflows...RNASeqGeneEdgeRQL and rnaseqgene which rely on edgeR quasi-likelihood and DESEQ2 respectively). I obtained different results I'm quite perplexed about, both in terms of number and identity of differentially...isPairedEnd=TRU…

edger deseq2 rnaseq de

updated 5.7 years ago • Raito92

Hi Mike, I have a question about the paired design. I have gone through vignette about linear combinations but could not achieve Pair adjustment with another factor. I am getting model being not full rank. Could you please help? Below is my design and what I try to achieve, ```r prep = c("L","D","D","D","L...gone through vignette about linear combinations but could not achieve Pair adju…

DESeq2

updated 4.4 years ago • Raj

I tried several time even using older version of R (3.5) to install bioconductor and deseq2 in my linux ubuntu 18 system but it is not working. I got the error like this- ``` 9: In install.packages(...) : installation of package...DESeq2’ had non-zero exit status

RiboProfiling DESeq2 Bioconductor RNASeqRData

updated 4.9 years ago • Taufiq

Hi there! I am using DEseq2 to perform different gene expression analysis. I was comparing in parallel - group A vs group B - group B vs group A When...the inverse logFoldChange value of comparison B vs A. I was wondering if this is true because other factors are taken into account during the computation of LogFoldChange . Best regards, Giulia

#DESeq2 #LFC #RNAseq

updated 2.9 years ago • giulia.lopatriello

I'm trying to export my CAGEset to a dataset for DEseq2 with consensusClustersDESeq2() but I'm a bit confused by how the grouping for the design matrix should be supplied...I'm trying to export my CAGEset to a dataset for DEseq2 with consensusClustersDESeq2() but I'm a bit confused by how the grouping for the design matrix should be supplied From...I'm trying to export my CAGEset to a dataset …

CAGEr

updated 4.8 years ago • MatteoP

to normalise my data. But I read that it is not necessary for the Differential Expression via DESeq2 since it has already a build-in normalisation on the data, is this correct? I read it in this article I believe: S. A. Michael

DESeq2 Normalization

updated 5.1 years ago • Bine

Hi, Briefly, I want to identify differentially expressed genes from RNA-seq data using DESeq2. I have three conditions and I want to compare the three conditions to each other. Usually, I perform pairwise comparison...building the dds file with the two conditions that I want to compare and subsequently I run DESeq2 on the dds object. I would like to ask if there are any differences be…

deseq2

updated 6.4 years ago • dequattro.concetta