Bioconductor Forum

I am new to R an DESeq2. I am trying to analyze differential gene expression of a paired-end RNAseq experiment. I did not do the alignment and...I am new to R an DESeq2. I am trying to analyze differential gene expression of a paired-end RNAseq experiment. I did not do the alignment and I am starting from a gene count matrix and a colData that I made I want to collapse replicates however…

deseq2

updated 5.8 years ago • jnaviapelaez

on SeqAnswers.</span> <span style="background-color:rgb(245, 245, 255)">Does anyone know how DESeq2 handles genes that have zero counts in one condition and >0 counts in another?</span> <span style="background-color:rgb...output shows that these genes have a positive log2 fold-change value, but I do not understand how DESeq2 arrives at this number if it is taking…

deseq2 deseq rna-seq

updated 11.0 years ago • gavrielmatt

I am writing to inquire about a problem I keep running into while running DESeq2. After running DESeq2 comparing two samples, I encounter an issue where I get >10000 differentially expressed genes...volcano plot for reference as well. Lastly, I've pasted my R Session below as well: library(DESeq2) > setwd("/Users/anjalimohan/Desktop/Research/Hikabe/") > list…

deseq2

updated 5.4 years ago • anjali_mohan

BP23 BP23P 2H Sample BP23P dsq$Status <- factor(dsq$Status, levels = c("Control","Stress")) dsq$Time.Point <- factor(dsq$Time.Point, levels = c("Before","After")) dsq$Sample.ID &lt...factor(dsq$Sample.ID) mm2 <- model.matrix(~ Time.Point + Time.Point:Sample.ID + Status:Time.Point, data = colData(dsq)) …

DESeq2

updated 23 months ago • DS

Hello, i am trying to install DESeq2 for R 3.1.3, but it is throwing an error : package ‘DESeq2’ is not available (for R version 3.1.3) I know R is updated tp 3.3 and

R bioconductor deseq2

updated 9.4 years ago • minie

Hi all, I have a bit of a theoretical question here. I'm using DEseq2 for DGE analysis between controls and a disease group. Within both groups, I have males and females. I've done DGE analysis...use the same step for the male analysis versus female analysis), while keeping the steps done in my first analysis as they are? Thanks

DESeq2

updated 2.6 years ago • marinaw

Hello, I am new to DeSeq2 and I am trying to use a multi-factor design to answer this question: **Is captured/input in condition 1 different from...captured/input in condition 2 ?** I used a combination of the DeSeq2 manual and https://support.bioconductor.org/p/61509/ to write the following script: ```r >print(MF_coldata) MF_condition

DESeq2 dese

updated 4.2 years ago • wilfried.guiblet

I have performed ChIP-seq for multiple transcription factors on samples from multiple patients. All ChIPs for each patient where sequenced on different sequencing runs (i.e...I have performed ChIP-seq for multiple transcription factors on samples from multiple patients. All ChIPs for each patient where sequenced on different sequencing runs (i.e. TF1...TF1, TF2, TF3 for patient 2 was on a separat…

diffbind

updated 7.3 years ago • Mthabisi Moyo

to see if any of the levels are impact any genes in an RNA-seq experiment.  I have been using DESeq2 to do differential tests.  I have been using the bestglm package. This is an example, I will scale this to the desired...I am not sure what to use with the theta parameter here, can I use the gene-wise dispersion from DESeq2.  Also is there a better "family " function t…

deseq2

updated 8.8 years ago • kodream

Dear all, In the vignette of GAGE pathway analysis package, a joint workflow with DESeq2 is shown, where only the column of log2 fold change from DESeq2 output is used as an input for GAGE. Is rlog matrix calculated...by DESeq2 applicable as an input for GAGE pathway analysis? Any comments would be appreciated. Best, Tom

deseq2 gage

updated 9.5 years ago • Tom

Hi everyone, first time poster. I have resorted to this because I can't seem to find substantive answers to my question (or don't exactly fit...with the hope we can answer both questions, but my concern is about aim 2. My plan is to simply use DESeq2 to identify differentially expressed genes, and then extract the results that pertain to our 20 genes, and discuss...all 20 genes and running so…

RNASeqData DifferentialExpression DESeq2

updated 2.1 years ago • Peri

<div class="preformatted">Dear all, My question is about the right design to use to perform LRT tests with DESeq2. I have two crossed factors, tra (2 levels) and pop (4 levels). I test the interaction term as follows: > ddsFullCountTable <- DESeqDataSetFromMatrix( + countData = countE, + colData = cda, + design = ~ pop*tra) > dds2inter.LRT <- DESeq(ddsFul…

updated 11.3 years ago • INRA - coutellec

Hello! We are using DESeq2 to analyse RNAseq data from an experiment and are running into convergence errors that we are unable to solve. We are...Hello! We are using DESeq2 to analyse RNAseq data from an experiment and are running into convergence errors that we are unable to solve. We are not sure what is causing these errors; and would preferably solve them rather than dropping the genes w…

DESeq DESeq2

updated 4.2 years ago • n.vandis

who are more experienced, and are authors/maintainers of packages, might consider using the 'good-first-issue' (or similar) tag on your repos even just for things like extra documentation that you might like but don't have time

Culture R GitHub

updated 3.5 years ago • BioInfoBeginnerrr

Hi All, I am new to DESeq2 analysis and I follow the [trinity](https://github.com/trinityrnaseq/trinityrnaseq/wiki/Post-Transcriptome-Assembly...Downstream-Analyses) pipeline for DESeq2 analysis. In that pipeline, [RSEM](http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-323) is...which generates the expected counts. These expected counts will be rounded off and later fed i…

RSEM deseq2 expected_counts raw_counts

updated 9.0 years ago • chudar.chudar

I was wondering how Diffbind deals with the problem of using multiple blocking factors (let's say, age, gender and postmortem delay). If there is a (small) limit of how many of those I could correct at the same time...interpretation). The cases I have seen in the tutorial are for when you only have one blocking factor. In the case that I have data for two or three variables at the same time, …

diffbind block regression deseq2 chipseq

updated 5.2 years ago • melnuesch

Modeling input data in ChIP-seq experiments with EdgeR, DESeq(2) or Limma][2] and [Question: DESeq2 for ChIP-seq differential peaks][3] and it seems like the general consensus is that normalizing against input is not...as repeat expansion had been previously observed with this mutation. 2. As suggested by the first thread I linked, it suggested that the change in input might be associated w…

deseq2 edgeR repenrich2 normalization

updated 5.7 years ago • mkmwong

Control 0 0 Control Control 0 0 ``` The first thing I did was to simply have my design be the Treatment Column like below ``` dds<-DESeqDataSetFromMatrix(countData

deseq2 r

updated 6.3 years ago • dtlloyd

presented a poster, being able to conduct differentially expressed circRNAs using STAR and DESeq2 (https://ash.confex.com/ash/2018/webprogram/Paper113333.html). But from my understanding, rRNA depleted samples may...because linear mRNAs are still viable in the pool. This brings me to 3 questions: 1) So DESeq2 is able to analyze circRNA? 2) But DESeq2 uses count method for analysis. Could …

STAR deseq2

updated 6.9 years ago • csijst

I have performed a diffential expression analysis on RNAseq data of 17 treated and 21 untreated samples using **DESeq2_1.22.2**. The results look good except for a gene showing a log2FoldChange < -20. I found a strong discrepancy between the DESeq2 log2FoldChange (-24.72) and the one calculated manually (-2.24). Have I missed something or why is there such a big difference? &…

deseq2 RNAseq

updated 6.7 years ago • Matthias Munz

into wells, and treated with one of the 10 possible combinations of the `` drug `` and `` dose `` factors.) --- In its simplest form, the goal of such an experiment is to compare the effect of the various treatments against the...untreated condition. One way to do this would be to add a `` condition `` pseudo-factor to the metadata, to encode each combination of drug and dose: <pre> …

deseq2

updated 9.3 years ago • kjo

Dear DESeq2 users, I ask for your advice: I am interested in using DESeq2 to evaluate effects of knockdown on gene expression during...Dear DESeq2 users, I ask for your advice: I am interested in using DESeq2 to evaluate effects of knockdown on gene expression during the course of differentiation. Below I have outlined my current approach, which is inspired by http://www.bioconductor.org/help/w…

deseq2 RNAi knockdown

updated 9.7 years ago • mmads09

Hi, When one have generated counts using FeatureCounts it generates a list of transcripts and note genes. I understand the procotol as "gene"-counts should be used - however how is genecounts defined? Can I use the transcript-count-lists as input in the DESeq2 analysis? Or should one convertet the transcript-counts (generated from featurecounts) to gene-counts? Is that what you are explaining i…

deseq2

updated 7.2 years ago • SannaG

I am running R 3.3.3 in RStudio.  I get the following error message when I try to load the DESeq2 library > library("DESeq2") Error in loadNamespace(j <- i\[\[1L\]\], c(lib.loc, .libPaths()), versionCheck = vI\[\[j\]\]) :   namespace ‘htmlTable...1.7 is being loaded, but >= 1.11.0 is required Error: package or namespace load failed for ‘DESeq2’ Help ple…

deseq2

updated 7.1 years ago • bslocum

with SAM. the Excel version does not seem to have the option to specify a value for s0 (the fudge factor). However in Siggenes, we can use the defaut setting (the fudge factor is computed automatically), or assign some values

siggenes ASSIGN siggenes ASSIGN

updated 21.3 years ago • Caimiao Wei

Dear Community, I have a question about the p-values reported by DESeq2. I performed differential expression analysis between cases and controls. The raw p-value reported for gene A with...Dear Community, I have a question about the p-values reported by DESeq2. I performed differential expression analysis between cases and controls. The raw p-value reported for gene A with the following FPK…

deseq2 normalization

updated 6.7 years ago • xianglongruoying

cells, and 24h (control) - yeast is growing alone. I need to do a time-series DE analysis with DESeq2. What I did is <pre> colData_yeast<-data.frame(time=factor(x=c(rep("0",2), rep("3",3), rep("12", 3), rep("24",3), rep("24c",2)),levels=c("0","3","12","24", "24c

DESeq2 time-series

updated 8.2 years ago • gtechbio

on a RNAseq dataset and found a strange problem in the result. The raw data set, the code, and the DESeq2 output were shared in a [Google Drive][1]. In the DESeq2 output, I ranked the genes by the ascending order of the column "padj...the normalized read counts of the 30 samples, calculated using counts(dds, normalized=T), to the DESeq2 statistics. When we examined the gene list, we found someth…

DESeq2

updated 5.0 years ago • Dejian Zhao

Dear DESeq2 Experts, I am new to the rna-seq data and I have started to learn DESeq2. I have used the following example to run&nbsp...DESeq2 http://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html\#count-matrix-input Then I extracted

deseq2 rnaseq rna-seq

updated 8.4 years ago • nikmehr22

treatments.  I have an OTU table and I'm trying to learn to normalize the counts in it using DESeq2. Ultimately, I want to obtain normalized counts for downstream visualization, clustering, and modeling. I have worked...MAplot.pdf?dl=0) This looks quite different from the example plots on page 10 of the DESeq2 vignette, and I suspect it's pathological. Next, I tried extracting the tran…

normalization deseq2 plotMA meanSDplot

updated 10.4 years ago • aravenscraft

I have a question about DESEQ2 data normalization.  I know that DESEQ2  requires raw reads counts, that the softwares normalizes by seq depth...for technical variation? Normally, I would quantile-normalize the data, but I understand that DESEQ2 does not support quantile normalized data, so how can I correct for this kind of variability?   Thanks in advance

deseq2 normalization

updated 7.4 years ago • marco.trizzino83

Am I misunderstanding the usage of `first()` and `second()` from the `GAlignmentPairs`. My understanding is that it should return the first and second mates for each pairs...TPC-29-37.bam") length(aln) # [1] 3164606 length(second(aln)) # [1] 3164606 length(first(aln)) # [1] 2 sessionInfo( ) R version 4.0.3 (2020-10-10) Platform: x86_64-pc-linux-gnu (64-bit) Running under: …

readGAlignmentPairs GenomicAlignments

updated 5.1 years ago • Marco Blanchette

Morning! I've just run DESeq2 on my RNAseq data with a dichotomous outcome, and I'm getting results that mean I have absolutely no deferentially...Morning! I've just run DESeq2 on my RNAseq data with a dichotomous outcome, and I'm getting results that mean I have absolutely no deferentially expressed...countData = data, colData = colData, design= ~condition) `` `` dds$condition <- factor(…

deseq2 adjusted pvalue

updated 8.2 years ago • hs.lansdell

Hi, I noticed that the order of factors in ```swish(x="condition")``` analysis makes a difference in the sign of the log2fc values. My question is which factor level...is the reference if for example one has two factors in the order ```MUTANT, WT``` for ```condition```. My assumption is ```WT``` is actually the reference level so a positive log2fc indicates

fishpond

updated 4.3 years ago • Jean

Using the pasilla dataset and the code from the vignette : ``` options(digits = 15) library(DESeq2) library(pasilla) pasCts <- system.file("extdata", "pasilla_gene_counts.tsv", package="pasilla", mustWork=TRUE) pasAnno...read.csv(pasAnno, row.names=1) coldata <- coldata[,c("condition","type")] coldata$condition <- factor(coldata$…

DESeq2

updated 4.5 years ago • Sam

to this but I still cant figure it out. I am trying to look at the interaction between two factors. The two factors are named Group and RFI. The dataset is listed below. I tried the phyloseq to deseq code which is below...phyloseq_to_deseq2(kostic, ~ RFI + Group + RFI*Group) This seems to work fine for the individual factors, but is wrong for the interaction I think. This is the output. I …

deseq2 phyloseq

updated 6.9 years ago • staffordvigors

<div class="preformatted">Naomi > Currently I am telling the biologists to consider microarrays as > screening experiments. Mostly, they use the results for second stage > analyses, which may be: ok. That's your choice. > e.g. statistical analyses such as clustering etc > bioinformatics analyses such as GO, BLAST or sequence analyses > lab analys…

GO Clustering GO Clustering

updated 22.1 years ago • Chad Shaw

Dear Michael, I would like to start by thanking you for the DESeq2 package and the support you give. Its remarkable. I have a doubt in the design formula that I would kindly ask your opinion...Dear Michael, I would like to start by thanking you for the DESeq2 package and the support you give. Its remarkable. I have a doubt in the design formula that I would kindly ask your opinion on.…

DESeq2

updated 4.2 years ago • nikolaus.virgolini

Hi all, I'm currently using DESeq2 (version 1.38.3) for my analysis and encountered a dispersion plot that appears quite different from the typical...Hi all, I'm currently using DESeq2 (version 1.38.3) for my analysis and encountered a dispersion plot that appears quite different from the typical dispersion...sex') samples_reorder <- samples[match(dirs, samples$sampleID), ] samples_re…

DESeq2

updated 22 months ago • Emma

I have multiple RNA-seq samples from 6 conditions and have to compare each condition against all the others: find genes dominant only in a specific group. I tried two approaches. First approach: separate all samples in 2 conditions: samples from one group vs samples from other groups, then repeat the operation...against all the others: find genes dominant only in a specific group. I tried two …

rnaseq deseq2

updated 7.8 years ago • Konstantin Okonechnikov

nbsp; When I ran this dataset through the original DESeq, considering time points as independent factors which I know is incorrect, I got thousands of differentially expressed genes. I feel like there is a better way to run...the model in DESeq2. There is no treatment between time series and running the model above in DESeq2 shows very few genes differentially...nbsp;     &…

deseq2

updated 11.0 years ago • stradermarie

Hi there! I am trying to perform a particular comparison after correcting for individual batch effects in DESeq2. The experiment involves the following samples: condition individual individual_by_group side di A A L di A A R di B...I am trying to perform a particular comparison after correcting for individual batch effects in DESeq2. The experiment involves the foll…

deseq2

updated 5.5 years ago • elisa.t.zhang

If there are multiple genes that overlap, I only want the first gene. Is there a way to do this in genomicfeatures already or do I need to preprocess the GTF file before calling makeTxDbFromGFF

genomicfeatures

updated 9.6 years ago • endrebak85

human genes in two groups of patients. (each group includes several samples) I am going to use DESeq2 to explore if there is any gene whose expression significantly changes between two groups. DESeq2, however, seems like...accepts only nu-normalized counts for the RNA seq. Is there a way to feed the DESeq2 with RPM data

deseq2 RPM gene expression

updated 6.7 years ago • ruhollah.mb

DESeq2 manual (http://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.pdf) says, on page 34: _By default

deseq2

updated 10.9 years ago • Peter Langfelder

I was wondering if there has been any more consensus recently on using DESeq2 to perform analyses of NanoString data? I have a NanoString dataset with 506 endogenous genes for four sample groups...and was looking for the best way to analyze the data. What if I just wanted to use DESeq2 to be able to normalize the count data from the Nanostring using VST to make PCA plots and heat maps for instan…

deseq2 nanostring

updated 7.6 years ago • casey.rimland

Hi,  I am finding an error with estimateDispersions() in DESeq2. In my experimental design I have 3 factors: Treatment, Time and Depth I start with a phyloseq object (PHYLUM) that I convert...to DESeq (Phylum) easily, including two of the factors in the design.   > Phylum=phyloseq\_to\_deseq2(PHYLUM,~ Time + Treatment) > Phylum class: DESeqDataS…

deseq

updated 11.3 years ago • sandramg82

in this languages are very limited but I needed to perform a certain analysis in it. I needed to use DESeq2, after many hours I finally got a working script. library(DESeq2) a = read.table (file = "superEnhancer_counts.txt",header...t",quote = F) dev.off() not the prettiest but it works ... But now I need to perform a DESeq2 analysis with paired samples. So two samples are fro…

R deseq2 Paired Samples

updated 6.9 years ago • m.wekking

div class="preformatted">Dear Bioconductors, I'm analyzing a microarray data set with three factors; cancer (yes or no, the interesting one), age and % tumour cells in sample. I'm interested to know how much each factor/coefficent

Microarray Cancer Microarray Cancer

updated 12.8 years ago • Robert Svensen

I have a couple of questions about estimation of dispersion in DeSeq2 vs. DeSeq. The paper and manual on DeSeq and DeSeq2 are very clear but I have a hard time understanding what is the ‘correct...mean, local or parametric)? is there a particular reason behind ‘tag-wise’ estimation not being in DeSeq2? Thank you

deseq deseq2 rnaseq

updated 11.1 years ago • JK

2 D628 3 GpB 2 D628 7 GpB 2 D628 28 GpB 2 . . . .</pre> With rep being a factor value for Animal-Group which distinguishes the individual nested within a group. I want to determine : 1/ Which genes...to the GpB? Here is what I did : <pre> Design_clean <- data.frame(Treatment=Group,Time=factor(Time), ind.n=factor(order$Rep),row.names=row.name…

deseq2 DESeq design and contrast matrix deseq

updated 7.8 years ago • SPbeginner

Hi! I tried to see how NB model is suitable for microbiome data as mentioned in DESeq2, I used this junk of codes. Could you correct me please, if I am out of the track? I used phyloseq object 'dietswap'. library...Hi! I tried to see how NB model is suitable for microbiome data as mentioned in DESeq2, I used this junk of codes. Could you correct me please, if I am out of the t…

deseq2

updated 5.8 years ago • wisam.tariqsaleem

I am using edgeR for an RNASeq experiment (~30 samples), where I need to explore the influence of 2 factors with 2 levels each (there are actually more factors, but for simplicity I put only 2 here): 1. disease_state (levels: control_0...and control_1) 2. localization (levels: A and B) I combined the factors and got 4 combinations: control_0.localization_A, control_1.localization_A, control_…

RNASeq edgeR RNASeq edgeR

updated 11.6 years ago • Mike Miller

Hi there, I'm one of the users of DESeq2. Recently I got a bunch of data with only raw read counts of RNA-seq. The design was quite weird. They applied the same procedure...Hiseq). If the procedures from fastq files to raw counts are the same, can I simply apply them into DESeq2 and find the results of differential genes? Thanks

deseq2

updated 7.6 years ago • krisd3v

Dear Community, I have a question about the voom-limma of RNA-Seq data analysis. I have multi-factor design with three factors: A (16 levels), B (2 levels) and C (three levels), and A is the random effect. My question is how to treat...manual. My code are given as below: design<-model.matrix(~A+B+C+A:B+A:C+B:C+A:B:C) Group<-factor(paste(Design$A,Design$B,Design$C,sep=".")) y&a…

limma

updated 9.2 years ago • Yanzhu Lin

Hi I am trying to install DESeq2 on Google Cloud Platform (Ubuntu 18.04.2 LTS; 4 CPUs; 15 GB RAM; `sessionInfo()` below) and get the following `non-zero exit...XML`, `annotate`, `genefilter`, or `geneplotter` individually. I successfully install DESeq2 on macOS 10.14.4 (Mojave). Any suggestions? Thank you Emilio **BiocManager Installed** ``` BiocManager::valid() [1] TRUE ``` …

deseq2

updated 6.7 years ago • emilio

samples in 15 hours (n = 30). To account for the association between mean and variance in RNAseq, we first used VST to normalize the expression level for each group separately, following this document: https://rdrr.io/bioc...DESeq2/f/vignettes/DESeq2.Rmd. After normalization with VST for each group, we find that there are difference for the overall

deseq2 vst variance

updated 6.6 years ago • Bitao Qiu

Dear Thomas, I was wondering if there is an easy way of using systemPipeR with DESeq2. Thank you   Ugo

deseq2 systemPipeR

updated 11.2 years ago • Ugo Borello

I would like help to make a code with the package TFBSTools. I want to find what transcription factors found in my DNA sequences. My sequences are in Fasta format. Thank you

TFBSTools RStudio R

updated 4.2 years ago • HELEN

I ran DESeq2 version 2.12.2 with the following code: <pre> Meta<-read.csv("BAT_Meta.csv",header=TRUE,row.names = 1) Raw<-read.csv...dds<-DESeqDataSetFromMatrix(countData = Raw,colData = Meta,design = ~condition) dds$condition<-factor(dds$condition, levels=c("old","young")) dds<-DESeq(dds) res<-results(dds) resOrdered<-res[order(res$pad…

deseq2

updated 9.6 years ago • nschaum