Bioconductor Forum

fold change of ”after treatment B” vs ” before treatment B”\].   I managed easily to apply DESeq2 for a differential expression of  ”before treatment X” vs ”after treatment X”, but now I have 2 result matrices that...pvalue, and I’m not sure if and how I should proceed and compare between them. I prefer that DESeq2 will do the entire required analysis from the beginning, if po…

Deseq deseq2 differential gene expression rnaseq statistical test

updated 7.9 years ago • Marina

I am unable to install DESeq2 package even after installing BiocManager. I have looked for various sources to find a tutorial video to solve this...I am unable to install DESeq2 package even after installing BiocManager. I have looked for various sources to find a tutorial video to solve this, yet I keep on receiving unable to write error. Can you give me step by step instructions what to do to g…

scRNAseq RStudio DESeq2

updated 2.4 years ago • DrFizz

Hi, I would to use DESeq2 to process three bulk RNASeq paired samples but I am trying to figure out what is the valid model to use here. I used tximport...to import Kallisto's transcript-level abundance estimates at gene level to use with deseq2. In the paired samples, the treatment is overxperssion of gene A. Sample information is as follows: ``` condition patient_…

deseq2

updated 6.5 years ago • Puks

data for about 23000 genes. The values are not integers. So, when I run the dds <-  on Deseq2, I got the following error: "some values in assay are not integers" Is there any commands in Deseq2 to fix this error? I mean...how I can use normalized data directly into Deseq2? Thanks

Deseq2

updated 10.0 years ago • mheydarpour

Mike Love, Simon Anders and I have been updating the DESeq package. This resulted in the package DESeq2, which is available from the development branch, and scheduled for the next release: http://www.bioconductor.org/packages...in order to not disrupt the workflows of DESeq users. For new projects, we recommend using DESeq2. Major innovations are: * Base class: SummarizedExperiment is used as th…

Normalization Classification Clustering DESeq cqn DESeq2 Normalization Classification cqn

updated 12.8 years ago • Wolfgang Huber

Hello, I want to perform differential expression analysis with DESEQ2 of my miRNA seq data. I want to include age, sex, height, gender, and the batch in the design matrix as a covariate. In our data...and must be removed. Please read the vignette section 'Model matrix not full rank': vignette('DESeq2')***** 1. My data has a total of 365 samples and 645 miRNA 2. I am adding each covar…

deseq2 miRNASeq designmatrix Batch

updated 5.8 years ago • anshulmbi

Dear all, I am trying to run DESeq2 in R 3.3.1. When I call library DESeq2 I get this: " Loading required package: GenomicRanges Loading required package

deseq2 DESeqDataSetFromMatrix software error

updated 7.6 years ago • nazaninhoseinkhan

After installing DESeq2 on a computing cluster in a user's account, (using the command "conda install -c bioconda bioconductor-deseq2"), I tried to...it had installed properly, but received the following error (please see bottom): ``` > library(DESeq2) Loading required package: S4Vectors Loading required package: stats4 Loading required package: BiocGenerics Loading...from ‘package:b…

deseq2 R3.6.1 library(DESeq2)

updated 6.3 years ago • adison.kleinsasser

log2FCs and p-values. acro.age.combined <- merge(acromegaly.results.age, acro.age.effect, by.x="row.names", by.y="row.names") Thanks, Quynh </div

updated 11.5 years ago • Tran, Nhu Quynh T

The reference for DESeq2's estimateDispersions() says that it uses Cox-Reid likelihood that was originally implemented in edgeR in 2010. I take...an offset, whereas CR can't. For that reason, counts have to be normalized prior to applying CR. In DESeq2 normalized counts are obtained by dividing the raw counts by the corresponding normalization factors: <span style...Small sample estimation o…

deseq deseq2 edgeR normalization

updated 10.1 years ago • Nik Tuzov

I have one  treated sample and one control sample of RNA-seq readcounts, can I use deseq2 for differential gene expression analysis? (I guess this can not assume the within-condition variation).  question2...such as\[ (A1,A2) (B1)\]   or   \[ (A1) (B1,B2)\] ), whether it is proper to use deseq2 question3:  Regarding the no replicat…

deseq2

updated 8.6 years ago • 247896572

was globally affected (shut down) and would like to learn more about the limitations of using DESeq2 on such data when it comes to calling differential expression. I believe such global effects can distort the assumptions...made by the statistical model behind DESeq2 and potentially make the downstream analysis heavily biased. Is there such an effect really at play? And what are the

deseq2

updated 5.7 years ago • kajocina2

Hi, I did DESeq2 for my data with simplified code: phyloseq_to_deseq2(phyloseq.genus, ~ allGroups). The variable allGroups consists

deseq2

updated 5.7 years ago • wisam.tariqsaleem

Hi, I just wanted an honest opinion on whether to include two groups together or analyse separately in DESeq2 (please see the pca plot using the link below). I am inclined towards analysing separately, but I want to hear from the readers...I just wanted an honest opinion on whether to include two groups together or analyse separately in DESeq2 (please see the pca plot using the link below). I am…

deseq2 group

updated 7.4 years ago • pokharel.kisun

I am learning DESeq2 and have a question of setting up design matrix for my experiment, I have 3 cells lines and each were treated with either

deseq2

updated 7.5 years ago • tombay82

controls and cases along with known co-variates like race, age, sex, RIN and library batch. So, in DESeq2 I could correct for these covariates as follows: dds=DESeqDataSetFromMatrix(countData=countData,colData=coldata...design=~race+age+sex+RIN+batch+condition) On the other hand, svaseq with normalized counts (within DESeq2) identified 13 variables for the same data. My question is regarding t…

deseq2 svaseq

updated 9.2 years ago • Akula, Nirmala NIH/NIMH [C]

I cannot get DESeq2 to download. I updated to the most recent version of R and get this issue ``` Error: package or namespace load failed for...I cannot get DESeq2 to download. I updated to the most recent version of R and get this issue ``` Error: package or namespace load failed for ‘DESeq2’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): there is no package called ‘R…

install packages R DESeq2

updated 3.6 years ago • eruan1

Hi there, I have googled for a few days now but am not getting there. Please help! Let's say I have the following dataset (2 conditions and 3 genotypes) and want to get differences between all genotypes (and ignore the condition). I run the following: <pre> # Generate example Data dds <- makeExampleDESeqDataSet(n=100,m=18) dds$genotype <- factor(rep(rep(c("I","II", "III"…

deseq2

updated 9.2 years ago • Nikolaus Fortelny

Hi All, I have 2 control and 2 treated replicates. I am running DESeq2 in order to identify differential bound regions form ChIP-seq samples. However, their are discrepancies in the enrichment...of the samples (ChIP-seq), which is messing with the results. Is their a way to ask DEseq2 to normalize the data and correct for the enrichment bias (maybe to correct for batch effect ) ? Many thanks, …

deseq2 chip-seq Differential binding

updated 9.6 years ago • p2016k

I have been using DESeq2 package for RNA-sq data analysis and really like the VST data in log2 units. But was unsure about usage of VST data for...scores with or without a given condition? I have generated batch-effect corrected VST data using DESeq2 and LIMMA. I understand VST data doesn’t take into account gene length whereas TPM does and may not be used to compare

DESeq2 VST

updated 4.1 years ago • AP

Hi, I see the advantage of using lfcshrink in DESeq2 analysis for getting a more "realistic" FC that takes into account the variance of the data. I have a question regarding...what variable generated by DESeq2 to use for the post-DESeq2 analysis. I run GSEA based on DESeq2 results in order to identify signatures enriched in one...compared to another, according to this "value". Till no…

lfcshrink GSEABenchmarkeR DESeq2

updated 2.1 years ago • delphine.rossille

Hi guys, I am new to R and DESeq2. When I am trying to install DESeq2 in R4.0.3, I encountered below problem. When I run "library(DESeq2)", it says can not load...Thank you! Code should be placed in three backticks as shown below ```r > library("DESeq2") 载入需要的程辑包：GenomicRanges 载入需要的程辑包：GenomeInfoDb Error: package or namespace load failed for ‘GenomeInfoDb’ in loadNamespace...Ge…

DESeq2

updated 4.9 years ago • Hui

Hi, I am trying to install DESeq2 on my Fedora but I am getting this error.     read.c:548:18: note: each undeclared identifier is reported only...library/Hmisc’ ERROR: dependencies ‘RcppArmadillo’, ‘ggplot2’, ‘Hmisc’ are not available for package ‘DESeq2’     \* removing ‘/usr/lib64/R/library/DESeq2’      …

deseq2 R fedora qiime

updated 7.4 years ago • kperlejewski

behaviours over time between the two conditions. Many thanks for your inputs ! Yvan library(DESeq2) countData <- read.table("counts_all.txt",row.names=1,header=T) countData_H58 <- countData[,31:90] ### data from table 1 to

updated 11.7 years ago • Yvan Wenger

Hey all,    I'm analysing a 16S microbial community dataset, and am using DESeq2 to test for differential abundances. When I do this, I supply raw count information to DESeq() as per the vignette rationale...scores below 0.05 being 'good' and above 0.15 being 'undesirable'.    I would like to use DESeq2 to test for differential abundance of PICRUSt-inferred g…

deseq2 picrust

updated 8.7 years ago • handibles

carrying out separate channel analysis of two-color data in limma. I find that I can not merge the duplicate spots on the arrays. The function lmscFit() does not provide an argument "ndups" to deal with the duplicate spots on...the arrays as lmFit() does. Therefore there are many duplicate spots in the DE genes. I wonder whether there is a way to merge the duplicate spots. Thanks Dejian <…

updated 17.0 years ago • De-Jian ZHAO

We have RNA-Seq data from different body parts; oral and aboral parts of small, medium and large sized specimens. We have mapped the reads using tophat2 and run cuffdiff and DESeq2 (with HTSeq count). Using the `` csDendro `` function in cummeRbund the samples cluster largely by oral/aboral parts, but clustering...small, medium and large sized specimens. We have mapped the reads using tophat2 and…

deseq2 cummerbund rlog fpkm clustering

updated 10.0 years ago • Jon Bråte

Hi there, Has anyone tried to use Sailfish estimated RPKM as input for DESeq2 for differential gene expression analysis? __Patro, R., Mount, S.M. and Kingsford, C.__ (2014) Sailfish enables alignment..._Nat. Biotechnol._, 1–6. http://www.ncbi.nlm.nih.gov/pubmed/24752080 I noticed that the DESeq2 article explicitly says "_DESeq2 performs analysis on counts of reads which can be uniquely assign…

deseq2 sailfish differential gene expression

updated 11.1 years ago • jceledon

I am working with RNA seq data. I would like to compute the residuals with DESeq2 to remove confounding effect in the data before running WGCNA.   We computed the residuals by using  DESeq2

deseq2 residuals wgcna

updated 8.7 years ago • glmazzo

So I output a matrix from DiffBind as my input into DESeq2, with the chromosome positions being removed from the count matrix, just leaving the first column key as a reference...colData, design = ~ sex + treatment)</pre> Following this I ran DESeq2 and have output the results as follows: <pre> write.csv(as.data.frame(results), file="results.csv")</p…

deseq2 deseq diffbind differential binding analysis

updated 8.0 years ago • rbronste

I has just started using Deseq2 to discovery deferentially expressed genes (DEGs). In my data, I have 6 strains (S2,S3,S4,S5,S6,S7), each of which was studied...analysis like this: 1) Upload counts data for all strains and all conditions (48 columns) to the deseq2 at once, performed comparison between "T1_S2_water" and "T1_S2_drought", and got 0 DEGs. 2) Upload counts data for T1_S2_water..…

deseq2

updated 7.0 years ago • naktang1

wikis.utexas.edu/display/bioiteam/Clustering+using+WGCNA>. It requires normalized counts from DESeq2 I used salmon to quantify the FASTQ data and then I used the salmon output as an input in DESeq2 to get the normalized...to be in the form of gene name and the normalized counts for each sample. What should I change in my DESeq2 procedure to get an output like that. [DESeq2 code](https://past…

deseq2 wgcna

updated 8.2 years ago • prab4th

if i get lucky) :) Hope that you are doing well. I am contacting you regarding the R package, DESeq2. I have been using this package for some years now, but only this week appeared a question when I was brainstorming with...In your paper "Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2" you have this statement: > while the VST is also effective at …

rna-seq deseq2 warnings nbinomWaldTest transformation

updated 5.5 years ago • andreia

div class="preformatted">Dear Michael, I am using DESeq2 for a factorial design. I have Celltype and condition as colData. I have used the formula ~ Celltype + Cellypte:condition...arises when I want to make an MA plot of the 2 conditions for one cell type. I call the function as DESeq2:: since I known there are some. Here is my code: > ddsFull class: DESeqDataSet dim: 54668 18 exptDa…

GO graph DESeq2 GO graph DESeq2

updated 12.2 years ago • Jose M Garcia Manteiga

I was wondering whether there was a way to take DESeq2 results and convert these to a DiffBind object for downstream processing? Thanks

deseq2 diffbind

updated 7.1 years ago • rbronste

pacbio sequel 2 machine and iso-seq3 analysis I have CCS reads of transcripts. Can I input them into DESeq2 for differential transcript analysis

deseq2

updated 5.6 years ago • pwnoyce

Would you like to tell me whether DESeq2 can analyze m6A-seq to detect differential m6A peaks? Other papers firstly used input reads to normalize m6A-seq reads...and then performed fisher’s exact test. It seems that DESeq2 can not accept normalized reads

DESeq2 MeRIP-seq

updated 4.1 years ago • BioEpi

Hello @mikelove , I used DESeq2 to find DE genes between 2 groups in our dataset. Now, I'm trying to see if the number of DE genes is significant. So I repeated...Hello @mikelove , I used DESeq2 to find DE genes between 2 groups in our dataset. Now, I'm trying to see if the number of DE genes is significant. So I repeated the following steps many times: 1. permute the sample labels (i.e. colu…

DESeq2

updated 2.3 years ago • michellewei

Hi everyone: I have a problem with the result of DESeq2 . When I dealt with case-control research, I used following commands . case=8 , control num=8. I just want the DEGs in case and...control.  > library("DESeq2") > countData <- read.table('featureCounts.txt', header=TRUE, row.names=1) > countData <- countData[ ,7:ncol(countData.…

deseq2

updated 7.6 years ago • linw

read counts of predicted circRNAs (back-spliced junction read) and now I was wondering if using DESeq2 for analysing the differential expression of those predicted circRNAs was a good approach, based on those counts

deseq2 circrna ciri ciri2

updated 7.6 years ago • sbcn

Hello, I'd like to preface this question by expressing my appreciation for this tool and the hard work that has gone into creating it. The flexibility in hypothesis testing that it provides is already amazing. So, thank you. What I'd like to know is if it is possible to test a joint hypothesis within DESeq2? For a use case, consider my experimental setup: I am looking at a parameter w…

deseq2

updated 6.6 years ago • nodice73

sum/average those samples and instead include them as a nested factor. The reason for this is those duplicates were from different sites within the same mouse. I had previously averaged technical replicates (same site, sequenced

deseq2

updated 6.0 years ago • mdsutcliffe5

seq dataset in which I am adjusting for subject age (design=~age+condition). I am wondering if DESeq2 generates a table of normalized reads after adjusting for the covariate, "age".  If so, how can I extract it? I ask because

deseq2 counts covariates

updated 9.8 years ago • hechtp

Hi all, I have a question regarding how robust DESeq2 is to large class imbalances for differential gene expression. I am currently analyzing RNA-seq data from the GTEx...I've found some of Michael Love's commentary on Bioconductor to be very helpful regarding how well DESeq2 can handle both low sample sizes and large class imbalances: <a href="https://support.bioconductor.org/p/101877/" tar…

deseq2

updated 7.1 years ago • munna.uppal

Hi everyone, I'm currently analyzing a RNA-Seq data using DESeq2. Looking at the FAQ's in https://www.bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html, concerning

deseq2

updated 4.9 years ago • andrebolerbarros

already read and read ... papers, questions in forums and i still have the same issue. I know that deseq2 has the independent filtering in the results() however after trying different alpha thresholds my results differs...is can i use the noiseq filter or just give the results that i got only with independent filter from deseq2? Thanks in advance

deseq2 noiseq lowcounts rnaseq

updated 5.3 years ago • andreia

Hi, I am using DESeq2 for analyzing an RNASeq Experiment. The details of the setup are as follows: I have two treatments for which I want to...is considerably higher than the variability in the other group (for same mean). If I understand the DESeq2 documentation correctly, the DESeq function fits one dispersion parameter per gene, not allowing for sample groups

deseq2 estimatedispersions

updated 10.7 years ago • hhoeflin

First, I know that DESeq2 is not meant to be run without replicates and results will not be meaningful. I am an analyst who has the following design...Condition - | - A | 1 B | 1 C | 1 A | 2 B | 2 C | 2 A | 3 B | 3 C | 3 I ran DESeq2 with LRT of ~Group + Condition vs ~Group to identify all DE features significant due to Condition. However my collaborators

deseq2

updated 5.8 years ago • august

needing to convert my alignment output (Salmon) into a matrix file (containing raw counts) used for DESeq2. I already have my phylodb and keggannot BLAST outputs and am hoping to merge these with the counts, lengths, and abundances...that on R on the cluster since my files are too big (25G) to use on R itself, but had realized that DESeq2 does not require me to normalize my counts and only requir…

tximport Normalization DESeq2

updated 4.6 years ago • johnsony

Hello, I am a novice for R and bioinfomatics. I am trying to run DESeq2 with my raw count table. I have been trying to follow the beginner's guide for the DESeq2 package, but it is still hard to...Hello, I am a novice for R and bioinfomatics. I am trying to run DESeq2 with my raw count table. I have been trying to follow the beginner's guide for the DESeq2 package, but it is still hard to under…

deseq2

updated 10.4 years ago • jjinhyoungkim

Hello, I have been trying to use makeTranscriptDbFromGFF() to read my gff file but I get the following error: extracting transcript information Error in .prepareGFF3TXS(data, useGenesAsTranscripts) :   Unexpected transcript duplicates In addition: Warning message: In .local(con, format, text, ...) :   gff-version directive indicates version is &nbsp…

genomicfeatures

updated 10.9 years ago • Miss Agnieszka Aleksandra Golicz

A vs condition B after controlling for the impact of the control condition. I think I need my DESeq2 design formula to assess (Condition A- Control) vs (Condition B - Control), but I'm not sure how to reflect that in my DESeq2

designformula DESeq2

updated 2.5 years ago • Grace.Ciabattoni

elements deregulation with SQuIRE. SQuIRE performs the differential expression analysis with DESeq2, but it does not allow you to introduce any batch effect. According to this and as I am analyzing samples of many laboratories...I have decided to perform the differential expression analysis with DESeq2 outside SQuIRE. This is the code (with the inputs modified by me) that I have extracted of …

SQuIRE deseq2 DESeq2

updated 4.3 years ago • fernandogs97

Hello A/Prof Love, Hope you are well and looking forward to CSAMA in the Italian Alps! After reading your comprehensive machine learning slides from BIOS 735 - Introduction to Statistical Computing (plus the HarvardX youtube videos with Prof Rafael Irizarry), we were hoping for one of the ML examples to use differentially expressed genes from RNA Sequencing analysis (please point in right dir…

DESeq2

updated 18 months ago • chris2.a.white

Hello all. I'm currently having issues loading DESeq2 into R version 3.6. I upgraded Bioconductor from version 3.7 to the latest version, 3.9. I am using my school's server...Hello all. I'm currently having issues loading DESeq2 into R version 3.6. I upgraded Bioconductor from version 3.7 to the latest version, 3.9. I am using my school's server to...conduct RNA-Seq analysis. **Here …

deseq2

updated 6.6 years ago • biancaineshoch

Hi, I have been trying to install DESeq2 v1.35.0 to replicate some data I generated some time ago, but I cannot find this subversion. BioCv15 has the v1.36, whereas

DESeq2

updated 20 months ago • Espresso

Dear all, I need to describe in more detail how the built-in transformation of data of the DESeq2 function normalises raw counts. Can anyone give me a reference to a paper where this has been described? I have not been

DESeq2

updated 4.9 years ago • Bine

Hey, with the method ""plotDispEsts" of the DESeq2 package one gets a two-dimensinal dispersion plot. Here I have the following question: Can somebody explain or does

deseq2

updated 9.9 years ago • voyager.85

Dear all, I'm a bioinformatichian and I'm using DESeq2 package. I have 2 requests: If I have a Multi-factor design, for ex. I have samples Normal and Treated in 3 different time

deseq2

updated 5.3 years ago • giovannaventola3es9

Dear all, I am new to RNA-seq analysis with bioconductor. I am wondering if I can use DESeq2 directly to perform survival analysis (e.g. Cox regression)? If not directly, do I understand correctly that we should

deseq2 survival rlog transformation

updated 8.1 years ago • array chip