Bioconductor Forum

am a PhD student and i would like to know if it is possible to find online the previuos versions of DESeq2 and where.Thank you. Best regards. Riccardo

DESeq2

updated 10.0 years ago • ribioinfo

successfully generated the simulation data using the function " makeExampleDESeqDataSet" of DESeq2,  But I have no idea to distinguish which genes are DEG and which are not

DESeq2 makeExampleDESeqDataSet

updated 10.5 years ago • boymin2015

Hello everybody, I have a question regarding the usage of DESeq2 for candidate analysis, so the targeted investigation of a pre-specified set of genes. In particular, I do have some...of a list of genes that I specified. My idea to approach this would be the following: 1) run DESeq2 on the whole genome data thereby incorporating the information from the whole genome to get more accu…

Bioconductor

updated 3 months ago • piffelpaff

nbsp; Hello Everyone,  I am using DESeq2 to look at differential gene expression. For some of the comparisons of interest, a strikingly low number of differentially...understand what is causing this difference in outcome and want to estimate gene-wise dispersion as a first step._ Is this possible? _ Here's what I have: <pre> object.DESeq <- DESeqDataSetFromMatrix(counts…

DESeq2 RNASeq differential gene expression

updated 8.5 years ago • A

I have encountered a curious bug that I haven't seen posted yet. When DESeq is rerun multiple times, it seems to multiply the metadata fields by the square of the `MulticoreParam`. By the second or third time it significantly grows the file size and slows the run time, fourth time it errors out. Can be fixed by setting `metadata(dds) = metadata(dds)[1]` after the repeated DESeq run. ```R librar…

deseq2

updated 6.3 years ago • rbutler

How scalable is DESeq2 to larger datasets?  I am running DESeq2 on a data set with 270 samples belonging to 10 sample groups.  But it takes

deseq2

updated 7.9 years ago • Steven Ge

patient and the goal is to detect DE genes over time or at specific time points. I have checked the DESeq2 vignette (section: Time-series experiments) but it is not clear to me how exactly DESeq2 models the correlation between

deseq2 timecourse

updated 8.1 years ago • Roula

Hello! I am following the ___Aaron T Lun et al. 2016___ paper to analyze my brain scRNA-seq data, but I am blocked in the step of gene filtering. I have my data in an _sce object_ and I have already filtered outlier cells (_isOutlier_) and genes based on low-abundance genes (with threshold 0.1 because we used UMIs and this is what they recommended). The last part is like this: ave.counts &lt…

size factor negative scran singlecellexperiment scater

updated 7.9 years ago • Marina V.V.

i have normalized the data using deseq2 internal normalization method. But it seems that my original input data is same as the normalized output. i don't know...on adjusted p value <0.1 Code should be placed in three backticks as shown below ```r library(DESeq2) library(tidyverse) count_data <- read.csv('rawcount_data2.csv',row.names = 1) head(count_data) colData <- read.c…

DESeq2 rnaseqGene Normalization

updated 20 months ago • sajadahmad41454

Hi, I have carried out differential expression analyses comparing conditions using DESeq2. Intuitively, I have considered genes to be expressed if they have a count of at least 10 in at least some libraries (sensu...in Condition1. What would be the best way to do this? From reading this site and the DESeq2 vignette, I know that the baseMean is "the mean of normalized counts of all sampl…

filter deseq2

updated 6.8 years ago • charles.foster

the results of my RNA-seq experiment. I have sequenced 57 samples. Each sample is described by 6 factors ( Timepoint, Sex, Treatment, Family, sequencing Lane and Run of extraction). I am struggling to find an effective way to...write a matrix design for such a high number of factor. My first idea was to create a design matrix as follows: f <- paste(data$TimePoint, data$Sex, data$Treatme…

limma voom multiple factor design limma voom

updated 10.1 years ago • oliver.selmoni

columns selectedIn addition: Warning messages:1: In maximumLevels(fac, n = length(colors)) : A factor was provided with 9 levels, but only the first 9 were used for coloring.2: In maximumLevels(fac, n = length(colors)) : A factor...was provided with 9 levels, but only the first 9 were used for coloring.3: In maximumLevels(fac, n = length(colors)) : A factor was provided with 9 levels, but o…

Microarray arrayQualityMetrics Microarray arrayQualityMetrics

updated 12.2 years ago • Lisa Cohen

Hello Michal, I realized that you used MLE to infer the parameters for DESeq2 model. I am just curious whether SGD is suitable to infer these parameters. Best

DESeq2

updated 2.9 years ago • BioEpi

Could you explain in simple terms what is the purpose of DESeq2 `unmix` function? What would be a scenario where it would be useful? What is meant by the `pure` components

DESeq2

updated 4.7 years ago • Sam

Hi, I want to set the p-value and LFC threshold to DESeq2 output results The way i understood is ```r independentFiltering = TRUE,alpha = 0.001 #will filter results for p-value 0.001...Also, how to identify upregulated and downregulated genes. The summary list by the p-value of DESeq2 run is as follows ```{r} res <- res[order(res$padj),] head(res) ``` ![results][1] In this, I assu…

DESeq2

updated 3.5 years ago • Shail

FC values with shrinkage values ``` model.str <- "~ genotype + individual" eset$genotype <- factor(eset$genotype, levels=c('WT', 'KO')) eset.model <- DESeqDataSet(eset, design=formula(model.str)) eset.fit = DESeq(eset.model...is doing what should be expected; but lfcShrink appears to be switching all the signs (as though the factor levels had been reversed) <a hr…

deseq2

updated 6.2 years ago • christopherlhartl

Dear Community,   I am writing to kindly ask support on the software deseq2. I am currently working on differential expression in transcripts of vitis vinifera. I aligned several RNAseq experiments...background-color:rgba(178, 255, 250, 0.65)">CAN3NI3\_exp.txt treated paired-end</span>   The first rows of my expression (reads count) input table (named expressionTabl…

deseq2

updated 8.2 years ago • scamiolo

an effect in the test distribution into a covariate used in IHW? More specifically, I have a set of DESeq2 results: P-values and Beta statistics for my predictor of interest. Separately I obtained DESeq2 results from a RNAseq...want to use the results from the second experiment as a covariate in IHW such that a p-value in the first distribution is weighted differently in the IHW calculation base…

IHW

updated 9.8 years ago • dhibar

I am analyzing a time series of a metatranscriptome. In metatranscriptomics, we have to do the regular normalizations found in RNA-Seq (ie. gene sequence length, and sample-differences in total expression). However, there is an additional normalization required to account for changes in species abundance. I would like to analyze differences in species-level transcript abundance, so I've done all…

deseq2

updated 8.4 years ago • jspmccain

div class="preformatted">Hi, the pileup function seems to stop doing the pileup after the first few sequences. For instance, if I test the function with my first 10 sequences it works fine: > start <- position(aln1)[sel...puprova) [1] 193 I manually checked that the result is correct. Then I repeat the process with the first 50 sequences > sel <- chromosome(aln1)…

PROcess PROcess

updated 16.8 years ago • David Rossell

div class="preformatted">Hi, I am having problems fitting a model (paired design with multiple factors) using limma, I have tried different ways of specifying the design and contrast matrix, but I stuck in the middle somewhere...eset, outdir=qc.dir, force = TRUE) # limma targets <- read.csv("targets.csv") targets pig <- factor(targets$Pig) pig type <- factor(targets$Ty…

affy limma affy limma

updated 15.2 years ago • Huang, Tinghua [AN S]

nest the replicates within the main groups OR set the replicates as a random effect when running the DESeq2. I am not particularly interested in differences between the replicates (we would like to assume that there are none

deseq2 Nested design random variable

updated 10.6 years ago • Silva

two different count matrices from salmon results, then merge them and import the final one in deseq2 (DESeqDataSetFromMatrix) considering to include in the final design formula the experiments from where the samples

deseq2

updated 5.2 years ago • sconosciuto

I use deseq2 to compare the transcriptomic signatures of 3 cell types composing the same tissue (A, B, C). The object "res" returns only

deseq2

updated 6.8 years ago • gilles.charpigny

to install a whole bunch of R packages. I thought it would be a breeze given the blank slate but the first package I'm trying to install and load, DESeq2, continuously fails. The problem seems to be the genefilter dependency...version of R (4.2.2). Should I just install R 4.2.1? This is what I am getting: ``` > library(DESeq2) Error: package or namespace load failed for ‘DESeq2’ in dyn.l…

DESeq2 genefilter

updated 3.2 years ago • Morgane

Hello, I have been trying to setup a HTML report of DESEQ2 analysis using ReportingTools and have encountered some snags. My DESEQ2 analysis has 5 conditions and I want to create...C vs CE RNASeq Analysis",title = "C vs CE RNA-Ssq Analysis of differential expression using DESeq2", reportDirectory = "./reports") publish(dds.dse, des2Report, .modifyDF=list(add.anns, modifyReportDF, ensemblLinks…

deseq2 ggplot2 reportingtools

updated 9.2 years ago • abass.conteh

Since `DEXSeq::estimateDispersions()` and `DESeq2::estimateDispersions()` are often the most time-consuming step of the two pipelines I was wondering if it was possible...to share the result of this between a (naturally paired) DTE and DTU analysis using DESeq2 and DEXSeq respectively or if they are indeed different? Cheers Kristoffer

DESeq2 DEXseq

updated 4.0 years ago • k.vitting.seerup

expression across/within sample groups. For now we have just followed the basic documentation of DESeq2. We used plotDispEsts which can indicate if the data works well with DESeq2 or not. The plot looks like this - ![plotDispEsts...output][1] From what I understand, this indicates that DESeq2 can work for the data, however why are there some gene-est which are at the lower left corner? Is it…

RNASeq DESeq2

updated 2.2 years ago • Karthik

Hello all, I have a large RNA-seq dataset that I am trying to run WGCNA on. The data set has many variables including (including 3 brain regions, 3 ages, sex, 2 genotypes.) I have been advised to use Deseq2 normalization for these samples prior to doing WGCNA. I am struggling with two aspects. 1) I assume I am not actually doing...including (including 3 brain regions, 3 ages, sex, 2…

RNASeq Deseq2 DESeq2 WGCNA

updated 4.1 years ago • jms2520

Say I have three samples with a simple design formula ~condition: sampleA - control sampleB - treatment (replicate 1) sampleC - treatment (replicate 2) DESeq2 returns one fold-change for control vs. treatment, but it is possible to consider separately control vs. treatment rep...condition: sampleA - control sampleB - treatment (replicate 1) sampleC - treatment (replicate 2) DESeq2 returns…

DESeq2

updated 4.5 years ago • P1000

Is it possible to conduct a linear regression analysis in DESeq2, where one could get a slope, r-squared, and p-value?  Based on this post (https://support.bioconductor.org/p/88254/) it...Is it possible to conduct a linear regression analysis in DESeq2, where one could get a slope, r-squared, and p-value?  Based on this post (https://support.bioconductor.org/p/88254/) it looks l…

deseq

updated 8.5 years ago • chimeric

Could you send me * The mysamples.csv file * The GM06986_peaks.bed.gz file (or just the first 100 lines or so) I'll take a look and let you know what the problem is. Cheers- Rory On 23/07/2013 17:11, "Giuseppe Gallone" <giuseppe.gallone...the possibility of using DiffBind with a Chip-exo dataset. The dataset is composed of transcription factor binding data for a large number of ha…

HapMap HapMap

updated 12.5 years ago • Rory Stark

any suggestions on how to integrate the two packages? Is it possible to estimate unwanted variation factors, e.g. with the RUVg or RUVr function from the transcript count matrix, and then add the obtained covariates along with

RUVSeq DRIMSeq

updated 2.8 years ago • Luca

3 [2]: https://www.nature.com/articles/s41588-018-0165-1 I am considering how to estimate size factors for samples correctly before model fitting. **edgeR** has `calcNormFactors` which tries to make some value like the median...calcNormFactors(countMatrix, targetLFC = c(0, 1, 0, 0), whichGenes = genesList) ``` Similarly, **DESeq2** has a function named `estimateSizeFactors`. Would provi…

edgeR DESeq2 Transcriptional Amplification

updated 6.8 years ago • Dario Strbenac

DNA synthesis. Can I just use the functions related to DNA synthesis (subset table) to do the DESeq2 analysis or I have to use the whole dataset and later found which over-representative functions relative to DNA synthesis

deseq2

updated 8.8 years ago • Pet Chiang

I would like to visualize how good is the fit of a model estimated using DESeq2, for instance by plotting the data along with the corresponding predicted values. Is there any equivalent of the \`predict

deseq2

updated 9.6 years ago • philippe.veber

objectives was to identify differentially abundant genes across my sample groups, which I did using DESeq2 I am wondering if its also possible to do some qualitative testing, based on the presence-absence of a gene and quantify

deseq2 limma

updated 9.3 years ago • adityabandla

lt;- read.csv("groups.csv", header=TRUE, row.names=1 ) #grouping targets group <- factor(paste(targets$Treatment, targets$Time, sep = ".")) cbind(targets,group=group) Batch <- factor(paste(targets$Batch, sep = ",")) #Make DEG

edgeR

updated 3.7 years ago • venura

the control consortium? To answer these two questions I would like to know if it is possible with DESeq2 to block one of the 2 variables, for example comparing for the consortium of strain n°1 the differents pH points to the...to keep only the results of counts of genes corresponding to the consortium of strain n°1 and use DESeq2 with a single variable, the pH? I tried some models like : …

DESe DESeq2

updated 2.5 years ago • Adèle

In a [previous question](https://support.bioconductor.org/p/85486/) I asked about how DESeq2 could be used to take the effects of sequencing from knockout (KO) tissue. This is possible by using interactions. If...In a [previous question](https://support.bioconductor.org/p/85486/) I asked about how DESeq2 could be used to take the effects of sequencing from knockout (KO) tissue. This is possible b…

deseq2 counts normalized counts

updated 9.5 years ago • snamjoshi87

I have 15 samples completed using miRDeep2 but need to upload files to R studio to get started on DESeq2. How do I input the files so I can start pre-filtering before the differential expression analysis

deseq2

updated 5.8 years ago • ljbond

Hi, first I want to thank you for creating limma package. I have a 2(Factor A)*4(Factor B) experimental design. I am trying to ask three...F Statistic), 3. Which genes are different between the levels of factor B given factor A (moderated t Statistic and log fold change), Example: (factorB_level2 - factorB_level1) under factorA_level1...lmFit(exprs_data, design_2) model2_bayes <- eBay…

limma

updated 14 months ago • Sudipta

or INFL3 against TCR+INFL3. It implied creating 4 different counts and metadata files and running DESeq2 4 times. Alternatively, I run all samples at once (in a single DESeq2 run) and extracted the desired contrasts with the...produce considerably different number or DE features. Here the numbers: With four individual DESeq2 runs (res <- results(dds): 11357 group_02_TCR_vs_01_c…

contrasts DESeq2

updated 2.6 years ago • jovel_juan

to quantify the reads. Therefore, I would like to normalize the reads in the different sample using DESeq2. May I know if there especial consideration that I should take before doing it. I mean I did not find anything related...to EXOM seq in the DESeq2 vignettes. Best AD

ExomeSeq DESeq2

updated 4.1 years ago • adR

Hello everyone, I am trying to install DESeq2 package in r version 4.0.2 but it doesn't work. I have searched a lot on different pages but I couldn't find a solution...BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("DESeq2") And the errors: * installing *source* package ‘RCurl’ ... ** package ‘RCurl’ successfully unpacked and MD5 …

DESeq2

updated 5.3 years ago • armin.shahpari

Hello, I have a question about how to design a formula. I have the following samples with three factors, Names, sample and condition. A total of 18 samples, divided into 9 groups(A-I), I want to use DESeq2 to analysis paired samples

deseq2

updated 5.3 years ago • Jessica

Hi everyone, Is there any script that links DE genes identified by DEseq2  directly to ReactomePA for Functional enrichment analysis? thanks much &nbsp

ReactomePA GO

updated 9.3 years ago • ta_awwad

Hi everyone, I am new in bioinformatics and when I try to use DESeq2 for my counts and further downstream analysis, I am faced with this problem. dds <- DESeqDataSetFromMatrix(countData

RNASeqData DifferentialExpression DESeq2

updated 2.3 years ago • Beyza

Hi ,   I recently installed the latest version of DESeq2 (VERSION 1.6.0) and upon running the command DESeq(dds), I receive the following error:   Error in ncol(mcols(dds)) : &nbsp

deseq2 bug

updated 11.1 years ago • ipurusho

How does DESeq2 account for the dependency between samples in repeated 16S data, for example, relative abundance for samples from

deseq2 repeated measures

updated 6.1 years ago • jperin

Hoping I can get some help. I have been using DESeq2 for several months now on several different projects (I manage a NGS core). For most of these projects, the samples do...Hoping I can get some help. I have been using DESeq2 for several months now on several different projects (I manage a NGS core). For most of these projects, the samples do not

deseq2 Euclidean sample distance

updated 8.6 years ago • gkuffel

Hello! If I wanted to conduct WGCNA analysis following a salmon/DESeq2 workflow, would it be appropriate to use the matrix generated after applying the vst function on the dds object? Something

deseq2 wgcna salmon

updated 7.1 years ago • maya.kappil

html?sid=9574bcdf-13ab-47a0-909b-1dfbb4dcf9ee> It seems that DESeq is better than DESeq2. What is yours opinion (expecially from the authors)? Thank you. Riccardo

deseq2 deseq

updated 9.8 years ago • ribioinfo

1) illuminahiseq_rnaseqv2-RSEM_genes*** file is the most suitable for subsequent analysis with DESeq2 imported through ***tximport***. There are 3 columns associated with each samples in the **1) illuminahiseq_rnaseqv2-RSEM_genes...it is estimated counts because data not in integer format***) column will be more appropriate for DESeq2 analysis imported via **tximport**. If anyone please co…

deseq2 tximport tcga rsem firebrowse

updated 5.7 years ago • J. Smith

Dear all! Sorry for yet another question on pre-filtering and DESeq2, but I didn't find anything related in the support pages... Now to my question: I know that DESeq2 does a wonderful job of automatic...interferes or violates the assumptions of the dispersion estimation (or any other assumption) in the DESeq2 model (Also considering that the pre-filtering in DESeq2 takes place after calculatio…

deseq2 pre-filtering

updated 10.8 years ago • Johannes Rainer

R version to 3.4.0 on a mac, after successfully re-installing sundry bioconductor modules, including DESeq2, when I load DESeq2 I get the following: library("DESeq2") Loading required package: S4Vectors Loading required package...masked from ‘package:base’:     apply Error: package or namespace load failed for ‘DESeq2’ in dyn.load(file, DLLpath = DLLpath, ...):…

deseq2

updated 8.7 years ago • afreedman405

matrix and replace AI1, AI2, AI4 by AI (and the same for AC) but it did not change. * I also used DESeq2 on thisdataset and I would like to compare results between DESeq2 and EBSeq (even if counting tables from RSEM are not...suitable for DESeq2 because they have to be rounded first) . In DESeq2, I selected DE genes at a p-value adjusted (method Benjamini) of 0.01 and

ebseq normalization differential gene expression

updated 9.6 years ago • jean.keller

of variation. From what I was read I understand FPKM is not ok here and I could use CPM or TPM or `DESeq2` median of ratios as [stated at hbctraining][1]. As I've used `DESeq2` previously the last option seems optimal for me. Also

DESeq2

updated 16 months ago • boczniak767

ind+grp+cnd+grp:cnd ~grp+grp:ind+grp:cnd ~grp+cnd+grp:ind+grp:cnd After reading the DESeq2 manual and forums I still did not understand the differences. My experiment design is: GROUP CONDITION ind.n s1 CONTROL

deseq2 interaction model

updated 5.6 years ago • aec

three biological replicates) be represented on the plot, instead of all three replicates.  In DESeq2 package I use:  library(ggplot2)  data <- plotPCA(rld, intgroup=c("clade", "strain"), returnData=TRUE)  percentVar

deseq2 pca plot

updated 9.0 years ago • pkachroo