Bioconductor Forum

Hi everyone, I’m using DESeq2 to analyze RNA-Seq data. I have basically 2 factors: Genotype and Treatment. I build the design matrix as ~ Genotype * Treatment

deseq2

updated 7.0 years ago • cihan.erkut

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 6.7 years ago • qwzhang0601

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 7.8 years ago • user31888

Hi,  The DEseq2 vignettes is very helpful, but I'd still like to confirm if my understanding to the contrast design for correlated...multiple group design. __ I could simply split the input dataset into subsets, e.g. running DEseq2 separately for each cell type (n=20), and report four results and later combined them e.g. using venn diagram.  design...design(…

deseq2

updated 7.9 years ago • Xianjun Dong

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 3.8 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 6.6 years ago • zefrieira

customizable_ figures). Tximport were used to load the count data from Kallisto into the DESeq2 pipeline. The first _runs_ with DESeq2 were pretty consistent with the Sleuth results (considering Sleuth...is more conservative than DESeq2) with 19 DETs for treatment1 and 34 for treatment 2. The highest/lowest log fold change was around 6.6 and -3. __BUT then...__The code…

deseq2 tximport rnaseq kallisto R

updated 8.7 years ago • birgittenilsson

a pipeline, so I followed his advice on making a Count Table of all the conditions and then run a DESeq2 a la RNA seq. Based on the discussion from his question on biocoductor (<https://support.bioconductor.org/p/72098/>) I am...GreyListChIP to remove the cell type/condition specific peaks from the Inputs and then running the DESeq2.  I know that diffbind has been designed for thi…

deseq2 diffbind csaw greylistchip chipseq

updated 7.2 years ago • Yonatan Amzaleg

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 8.9 years ago • jogiles

are my code <pre> AMHdup<-read.csv(file="count_genes_8indi_RmDup.csv", sep = ";",header=TRUE,row.names=1 ) library(DESeq2) library(HTSFilter) coldatafile<-read.table(file="colData.txt",sep="\t",header=TRUE,row.names=1

deseq2 colData rownames

updated 9.7 years ago • cagenet34

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 6.0 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 8.3 years ago • stevenn.volant

Dear users, Instead of counts (non-negative integers) required by DeSeq2, I have negative numbers and fractions, and I need to use DeSeq's statistics to find out significantly up/down genes...Dear users, Instead of counts (non-negative integers) required by DeSeq2, I have negative numbers and fractions, and I need to use DeSeq's statistics to find out significantly up/down genes. Since

deseq2 logfoldchange

updated 9.3 years ago • rraadd_8

Hi I'm having an issue with DESeq2 results.  I'm working with 2 cell lines from different patients and originally I created a .csv excel file with both...SerialParam()) \#Add column as listed in sample.csv colData(se)$group= sample$group \#Run DESeq2 with variables library(DESeq2) dds<-DESeqDataSet(se, design=~group) dds<-DESeq(dds) \#Results that contr…

deseq2 results rstudio

updated 10.6 years ago • Lillyhchen

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 12.5 years ago • Guest User

Hi Michael or DESEQ2 community, First, sorry, I'm not sure why the images don't load, but if you right click on them they will. When I use the DESEQ2...Hi Michael or DESEQ2 community, First, sorry, I'm not sure why the images don't load, but if you right click on them they will. When I use the DESEQ2 results() function I get a variable called *stat*, which is useful for GSEA. ![Resu…

deseq2 stat lfcshrink

updated 5.9 years ago • divercory

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 5.7 years ago • jabaron.phd

rarefactions  Instead consider implementing some of the differential expression analyses in the DESeq2 package for R. R2. The DeSeq2 method should be used to highlight differentially abundant OTUs. Which method would you

deseq2 microbiome fungi fungal microbiome

updated 7.8 years ago • david.gramaje

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 7.9 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 7.8 years ago • owen.whitley

Hi, I would like to ask that the deta input fort Deseq2 is required a count metric. However, after I look into my count data, I would that there is a batch effect in my count data...represented the treatment.][1] How should I normalized my read count data before applying in Deseq2 and for WGCNA analysis. Currently I have tried using Combatseq on raw read count before using in Deseq2 analysis…

DESeq2 WGCNA Normalization NormalyzerDE BatchEffect

updated 3.0 years ago • suphamon.j

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 8.4 years ago • rrcutler

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 6.6 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 8.7 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 9.5 years ago • yjliu1127

Hello, I apologize if this question was answered many times before. I'm a little bit confused by DEseq2 coefficient. I have two factors, genotype (WT, KO) and batch (B1, B2, B3) variables and would like to see gene expression between...Hello, I apologize if this question was answered many times before. I'm a little bit confused by DEseq2 coefficient. I have two factors, genotype (WT, KO) and ba…

DESeq2 coefficient

updated 2.0 years ago • J

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 4.9 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 10.0 years ago • Jon Bråte

Hi there, I want to use DESeq2 for differential peak detection for ChIP-seq data. I know there are many methods implemented for this purpose&nbsp...github.com/crazyhottommy/ChIP-seq-analysis\#differential-peak-detection Diffbind internally uses DESeq2 and EdgR, but I want to take the other way: Say I have untreat and treat group for my ChIP-seq data, each with three replicates...nbsp; 45 …

deseq2 deseq chipseq

updated 8.7 years ago • tangming2005

Dear the bioinformaticians, I am using DESeq2 to normalize data from 100 samples from 100 patients. The 100 samples are classified into 3 groups (group A; 30 samples...to compare significance of gene expression among each group. In statistics, we use ANOVA, but in DESeq2 there is no option to compare gene expression among more than three groups. 1. So, my first question is "Is it ok to 1) obt…

DEseq2

updated 2.9 years ago • Changsuk

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 4.2 years ago • mithu18mohan

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 4.1 years ago • IamFrofro

My first post to this forum, as requested.] I cannot perform data.table revdep checks because DESeq2 was unavailable in Bioc-devel (3.11). https://bioconductor.org/packages/devel/bioc/html/DESeq2.html The build error...bioconductor.org/checkResults/devel/bioc-LATEST/lpsymphony/malbec2-buildsrc.html In the meantime, DESeq2 has removed the IHW Suggests dependency so that DESeq2 will propaga…

lpsymphony IHW

updated 6.3 years ago • mattjdowle

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 4.5 years ago • michael.morash

Hello there, I am trying to analyse a dataset using deseq2 with kallisto via tximport. I am using the following code: tximport(files, type = "kallisto", tx2gene = tx2gene, ignoreTxVersion...differential gene expression (DGE) methods. The first method, which we show below for edgeR and for DESeq2, is to use the gene-level estimated counts from the quantification tools, and additionally to use t…

kallisto tximport deseq2 counts

updated 5.9 years ago • Mozart

peptide epitopes. Samples usually include 8 or more negatives (no antibody) and other samples (in duplicate). We're interesting in comparing each of the other samples individually against the negative samples to find peptides

DESeq2 PhIP-seq

updated 2.9 years ago • Samantha

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 7.4 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 7.8 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 4.8 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 5.2 years ago • rbronste

I have samples from 1 experiment (experiment A) distributed in 2 sequencing runs. This experiment consists of 3 biological replicates, and the first replicate has 3 technical replicates, which I collapse using the collapseReplicates function. Moreover, the 2nd sequencing run contains also samples from a different experiment (experiment B). Now I want to analyse the experiment A using DES…

DESeq2

updated 4.1 years ago • turtle012

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 7.0 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 9.0 years ago • Mike Miller

are still before fitting in the analysis. Is it possible to obtain the post-fitting counts from DESeq2 analysis?  Thanks     &nbsp

deseq2

updated 10.0 years ago • pchiang5

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 7.0 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 5.9 years ago • Raito92

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 5.1 years ago • Taufiq

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 5.2 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 6.6 years ago • dequattro.concetta

New to DESeq2. I am using DESeq2 to normalize data for some microbiome and eDNA metabarcoding projects. My datasets are observational...I'd also like to do more analyses with machine learning on other ecological factors. When running DESeq2, should I incorporate all factors of interest in the design (e.g., ~ sex + age + reproductive status + season)? Or is there a way

DESeq2

updated 3.3 years ago • Devin

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 10.1 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 10.6 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 5 months ago • piffelpaff

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 8.0 years ago • Steven Ge

Hello, My team and I have a question regarding the addition of covariables in DESeq2 analysis. We ran DESeq2 with a first model and obtained adjusted p-values for all genes. However, when we tried to add 2

deseq2

updated 5.6 years ago • andree-anne

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 8.3 years ago • Roula

Dear all, I am attempting to perform DESeq2 analysis (using the Geneious plugin) for targeted RNA-seq of several hundred genes. Only the target set of genes is sequenced...sure that it is not biological. I think there are several possible causes, one of which might be the DESeq2 analysis, and so I would like to rule that out if I can. A colleague recently informed me that DESeq2 is not well s…

DifferentialExpression DESeq2

updated 4.1 years ago • dadca596

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 3.1 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 4.9 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 3.6 years ago • Shail