Bioconductor Forum

Hi Michael, I am using deseq2 to perform DE analysis over ~100 human postmortem brain tissues, our major interest is finding DEGs between AD and...secsectitle0015 According to this result from GTEx dataset, a bunch of sequencing-related technical factors appear as top drivers of expression variance for gene count matrix, which means a better model should include these...technical factors as wel…

DESeq2 variancePartition

updated 2.8 years ago • Weiqian

Hi everyone, I'm hoping for some help modeling an RNA-Seq analysis in DeSeq2. I have 4 populations (A,B,C,D) , and initially I used the following to compare them each to one another: >dds <- DESeqDataSetFromMatrix...AvsB, AvsC, AvsD, BvsC, BvsD, CvsD. Now I'm interested in (A-B)-(C-D), is this possible in DeSeq2? Would limma or ballgown be an alternative? Thanks fo…

deseq2 limma

updated 6.2 years ago • Jonathan.allen

Hi, We are trying to understand DEseq2 fold change values. Here I am giving example of some genes with their normalized read count values and calculated...Hi, We are trying to understand DEseq2 fold change values. Here I am giving example of some genes with their normalized read count values and calculated log...Hi, We are trying to understand DEseq2 fold change values. Here I am giving exa…

deseq2

updated 8.3 years ago • madhusudhana.janga

Hi guys, I tried to get the colData from the GSE dataset I have downloaded with GEOquery. I have two problems to solve. 1. How to get the counts table from the dataset? 2. How to prepare for the colData that the DEseq2 package asks for? Here's what I have done. First I downloaded the dataset in the matrix form and transform into expression set to have a look at the table. ```r gse…

GEOquery DEseq2

updated 3.6 years ago • Yugang

Dear all, I would very much appreciate any assistance in the analysis of our RNA-SEQ data, i feel that i'm making a mistake somewhere but cant quite lay my finger on where this is happening.  __Study design:__ 8 wasp allergic patients were stung by a wasp, peripheral blood samples were drawn before the sting (T0) and at 5 set time points afterwards (T5, T11, T15, T30 and T60 mi…

rnaseq deseq2 timecourse

updated 9.1 years ago • cannedcanary

Dear community, a quick question on how fold changes are calculated in DESeq2. Below I have the counts for a gene X in 5 treatments and a control, with 4 replicates: Control : 1 0 0 0 Treatment 1: 1 3 475 0...Dear community, a quick question on how fold changes are calculated in DESeq2. Below I have the counts for a gene X in 5 treatments and a control, with …

DESeq2 RNASeqData

updated 4.6 years ago • GlycineMax

Hi - is it possible to correlate gene expression patterns with a linear numerical factor in DESeq? Here's the background: I have used DESeq to analyse gene expression in 40 RNAseq samples; three sample groups...clusters, but this clustering pattern or sample grouping does not correlate with any of the known factors I have for the samples. I have an image which shows this pattern - not sure how to…

deseq2 correlation deseq linear

updated 10.4 years ago • matt.arno

When running differential expression analysis using DESeq2 the highest rank gene has a p value of 0. What is the lowest p value that can be reported by DESeq2

deseq2

updated 8.7 years ago • rw6

Hello, I am have ChIPseq data from histone marks from 2 different condition (mock and treated with 2 biological replicas each) and the aim of my analysis is to study whether a particular histone mark is enriched in one condition versus the other. I am new to bioinformatic and I don't have any statistical training and I am trying to teach myself how to normalise the data and perform the diff…

DESeq2 ChIPSeq DiffBind edgeR HistoneModification

updated 2.8 years ago • Giulia

pre> Now, the same analysis does not yield these groups anymore but comparisons with "\_vs\_" (DESeq2 v1.18): <pre> > resultsNames(dds_withint_forgroupanalysis2) [1] "Intercept" "group_controlmat_vs_controlelo" "group_controlmer_vs_controlelo...for all possible contrasts? Now I have to do contrasts where I compare all the groups (related to my first questi…

deseq2

updated 7.8 years ago • Jonas B.

Seq) after degradation of my protein of interest. I am currently using Diffbind in combination with DESeq2 method of dba.analzye() but diffbind provides so many different options for dba.normalize(), I am not sure what to use...CTCF_narrowpeakscount, method = DBA_DESEQ2, normalize = DBA_NORM_RLE) #print out the normalization factors norm <- dba.normalize(CTCF_narrowpeaksnormalized, bRetr…

GenomicLocalization DESeq2 Cut&Run Diffbind Normalization

updated 5.0 years ago • Monica

In my project, we performed a RNAseq of pig embryos, whose mothers were supplemented or not with arginine on diet. We are trying to analyse the differential expression of this data using DESeq2 with a nested model: Y= mean + Sex + treatment + Sex by treatment interaction + mother within treatment + error , but it is not working...not with arginine on diet. We are trying to analyse the differen…

deseq2

updated 6.9 years ago • susana.amaral.teixeira

how to used design matrix in edgeR to  perform differential expression analysis on continuous factor. Here is the description of my data. I have one __continuous__ factor measuring the level of __protein...analysis. But i am not sure how to interpret </span>the logFC calculated here. Since the factor here is continuous, do we still interpret it …

edger design matrix continuous

updated 7.6 years ago • ashley.lu

I don't understand how DESeq2 calculates the p-values given by `DESeq2::results()`. I thought it was 2 * pnorm(abs(log2FoldChange / lfcSE), lower.tail = FALSE...with `log2FoldChange` and `lfcSE` taken from the corresponding columns of the output table given by `DESeq2::results()`. However, when calculating the p-values this way, I get non-negligible differences (i.e. not only numerical ina…

deseq2

updated 6.4 years ago • Homer

Hello, I'm using DESeq2 to analyse a large dataset with basically three predictors: 1 - Subjects = the ID of the subject involved in the experiment...explained by the three predictors for each gene to categorize them based on the most influencing factor (this is only an exploratory analysis). Following the DESeq2 manual, the paper, and [this](http://seqanswers.com/forums/showthread.php

deseq2 analysis of deviance

updated 7.8 years ago • Giovanni Bacci

Hi everybody, right now Iam trying to analyse my MeDip data set using Diffbind and Iam quite confused whather to use edgeR or DESeq2 for the analysis (iam a biologist with zero training in statistics and bioinformatics try to teach himself all the stuff). I tried already both options and DESeq2 gives me ~15 % less differential methylated sites. However Iam not sure how to judge if I get ride of …

diffbind medip-seq edger deseq2

updated 8.2 years ago • florian.noack

gt;To: bioconductor at r-project.org >Subject: Re: [BioC] [DIFFBIND] batch effects and blocking factors >Message-ID: <53A9460F.9020608 at dpag.ox.ac.uk> >Content-Type: text/plain; charset=ISO-8859-1; format=flowed...3 samples). I would like to run a multifactorial analysis to >> regress the batch effect first, and then possibly analyse any remaini…

DiffBind DiffBind

updated 11.5 years ago • Rory Stark

impacts subjects from group B vs. subjects from group A at any time post-treatment. The first challenge is to create a DESeqDataSetFromMatrix because the design function ~ Group + Time + Group:Subject.nested + Group...to address this by using a custom model matrix for DESeq, but I need to create a DESeqDataSet object first - so I run DESEQDataSetFromMatrix call using 'ignoreRank=True'. The…

DESeq2

updated 4.9 years ago • Nashla

deal with an experimental design comprising both categorical (strain A/B) and numeric (time 0/2/4/10) factors. Is Bioconductor offering specific solutions for this? I was looking into the lme function of the nlme package and

updated 16.7 years ago • Paco Recca

also looking at floral and meristematic tissues, but I’m having a hard time figuring out how to use DESeq2 to make all the appropriate comparisons. I’ve seen posts like https://support.bioconductor.org/p/58893/, as well as looking

DESeq2 RNASeq

updated 3.9 years ago • Matthew

Hi! I am trying to perform differential expression analysis comparing multiple groups at the same time. My sampleTable is the following: Name Condition Differentiation AF_MSCs_1 AF_MSCs_1 AF_MSCs low AF_MSCs_2 AF_MSCs_2 AF_MSCs low AF_MSCs_3 AF_MSCs_3 AF_MSCs low F_MSCs_1 F_MSCs_1 F_MSCs medium F_MSCs_2 F_MSCs_2 F_MSCs medium F_MSCs_3 F_MSCs_3 F_MSCs medium…

deseq2

updated 5.7 years ago • dequattro.concetta

things, but can't figure it out I think it has something to do with it not correctly reading the first column that has the gene names and the first row that has the names that correspond to who the count values within the...matrix belong to, but don't know how to fix it > library("DESeq2") > > > gene_count_matrix <- > as.matrix(read.csv("/home…

deseq2

updated 6.5 years ago • skamboj

Hello, I have made great use of your DESeq2 package and grateful for it. I have recently normalized using conditional quantile normalization to remove gene...Hello, I have made great use of your DESeq2 package and grateful for it. I have recently normalized using conditional quantile normalization to remove gene length bias. This CQN normalization gives me log expression data that includes …

CQN deseq2

updated 6.1 years ago • nicholas.macknight

<div class="preformatted">hi all -- does anyone know how to turn off the forced conversion of character vectors to factors when merging with IRanges::DataFrame objects? in the example below fooX.df is a base data.frame, while fooX.DF is the...hi all -- does anyone know how to turn off the forced conversion of character vectors to factors when merging with IRanges::DataFrame objects? in the …

updated 12.4 years ago • Murat Tasan

Hello, I would like to ask two questions: 1) After using the DESeq2 normalization it is possible to compare the expression of the same gene among samples but it is not correct to compare...genes in the same samples. To do that is better to generate TPM but they are not as good as the DESeq2 nomalized values if you want to compare the expression of the same gene in different samples. Is the …

deseq2

updated 5.4 years ago • ribioinfo

Hi, I'm new at bioinformatics and use DESeq2 for the first time. I'm analyzing a RNA-seq data - 3 WT replicate and 3 mutant replicates. The MA plot show diagonal lines...too nit to me. any ideas? picture in the link https://www.scribd.com/document/394171998/MAplot-DESeq2-Res thanks in advance

deseq2 MAplot

updated 7.1 years ago • avitalwasser

analysis on 3 vs 3 (3 biological replicates). This is my script using Rstudio: library('DESeq2') directory<-'/Users/htseq/A16_AE11' sampleFiles<-list.files(directory) sampleCondition<-c('A161','A162','A163','AE111...sampleTable=sampleTable, directory=directory, design=~condition) colData(ddsHTSeq)$condition<-factor(colData(ddsHTSeq)$condition, le…

DESeq2

updated 4.7 years ago • polaxgr

Hi DESeq2 Community, I'm currently working on a comparison of drug effects on tumour and wild-type cells. I have tumour cells from...M") dds$Treatment <- relevel(dds$Treatment, "0") dds <- DESeq(dds) Here is my first question: from what I understand, this design is accounting for patient difference. So I think I don't need to build a design...or female (if I wanna keep …

deseq2

updated 9.7 years ago • dustar1986

I am using DESeq2 and have a genes x counts matrix where some of the columns are technical replicates. I want to use collapseReplicates...the raw counts table) the documentation( http://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html) says "DESeq2 provides a function collapseReplicates which can assist in combining the counts...the R link makes it sound like it's o…

deseq2

updated 6.4 years ago • wiscoyogi

We have performed differential expression analyses using DESeq2 to directly compare the same tissue in two species that diverged from a common ancestor about 50 million years ago...We have performed differential expression analyses using DESeq2 to directly compare the same tissue in two species that diverged from a common ancestor about 50 million years ago. We added a line of code that takes int…

deseq2

updated 5.4 years ago • adi.saxena

Hi guys! I want to know if edgeR also need to specify reference group data similar to DESeq2? Because DESeq2 need to use ``` dds$condition <- factor(dds$condition, levels = c("untreated","treated")) # or dds$condition <- relevel...group. But I didn't find relevant info when read the edgeR manual.I just find ``` group <- factor(c(1,1,2,2)) ``` but didn't clearly spec…

edgeR reference group

updated 6.2 years ago • 15958021290

Hello,  I'm analysing an RNA-seq dataset using DESeq2, and would like to inspect the top three principal components on a 3D PCA plot. I know that the plot PCA function has been...with(samples,data.frame(shortname = I(shortname), condition = condition, donor = donor)) #start DESeq2 library("DESeq2") #construct your DESeq2 data set, making sure to specify the design matrix here dd…

deseq2 rnaseq PCA

updated 10.7 years ago • erin.gill81

Hi, I know that DEseq2 can do low counts filtering but I wanted to set my threshold based on CPM values rather than count values then...Hi, I know that DEseq2 can do low counts filtering but I wanted to set my threshold based on CPM values rather than count values then do...filtering. Is there a way in DEseq2? Thanks for the help. J

deseq2

updated 9.8 years ago • John

a> I installed all packages as your guidelines (<a href="https://angus.readthedocs.io/en/2017/deseq2-asthma.html" target="_blank">https://angus.readthedocs.io/en/2017/deseq2-asthma.html</a>) now I am running your scripts

deseq2 Tutorial

updated 7.7 years ago • krwyaong.ju

I am trying to do some analysis with DESEq2. I can run the analysis and get my results. However, I am concern about the table I have been using to input the read counting...data into DESeq2. <span style="line-height:1.6">The read counts was done by another person using GFOLD. The GFOLD output is a table with...deleted the unwanted rows and created a .txt file with Gene Symbol and R…

deseq2

updated 11.3 years ago • alantb_cederj

Hi all, I'm stuck in a strange result while doing DESeq2 tutorial with tximport and tximportData.  The script I used is below: library("DESeq2") library("tximport") library...txi.rsem$length[txi.rsem$length == 0] <- 1 sampleTable <- data.frame(condition = factor(rep(c("A", "B"), each = 3))) rownames(sampleTable) <- colnames(txi.rsem$c…

deseq2 tximportdata tximport

updated 7.6 years ago • changhan1110

gene after normalization. Should I just need to divide the count of each gene by the normalization factor for its library? Then, I may use the normalized data for DE analysis and other further analysis (e.g. clustering). Thanks

Normalization Normalization

updated 15.5 years ago • 王喆

use the FPKM I can compare the expression across different samples and different experiments. With DESeq2 I can compare the expression of the genes that are in the normalized table. How can I use the DESeq2 normalization and

deseq2 normalization

updated 9.9 years ago • ribioinfo

Hello All! I am running DESeq2 on my RNA Seq dataset. I have four groups in my treatment with 8 replicates and about 14,500 rows (genes) after using keep...Hello All! I am running DESeq2 on my RNA Seq dataset. I have four groups in my treatment with 8 replicates and about 14,500 rows (genes) after using keep (removing low copy numbers) and removing NA. I also used level so that my Control…

Normalization RNASeq DESeq2

updated 2.2 years ago • erika.maldonado-rosado

Dear all, I am used to analyse RNA-seq data with the very useful and well-documented DESeq2 package. I have analysed an RNA-seq dataset containing 2 conditions (control and transgenic mice) with 3 replicates...is a 2 against 3 experiment and therefore the statistical analysis applied is not valid“. As in the DESeq2 Genome Biology article: « experimental design with as little as two or …

deseq2

updated 10.8 years ago • celine

DepMap_ID)) [1] TRUE tar3$TypesRas<-paste(tar3$Types,tar3$RAS,sep="."); tar3$TypesRas <- factor(tar3$TypesRas) mydata3<-round(mydata3) library("DESeq2") dds <- DESeqDataSetFromMatrix(countData = mydata3, colData...tar3, design = ~TypesRas) colData(dds)$TypesRas <- factor(colData(dds)$TypesR…

DESeq2 DEGs

updated 4.5 years ago • Ming Yi

to contrast treated 1,2,3 against 2 controls, and treated 4 against 2 controls. (condition <-factor(c("treated1","treated1","treated2","treated2","treated3","treated3","treated4","treated4","control1","control1","control2","control2...txi.g, colData=coldata, design=~condition) dds <- DESeq(dds) res <- DESeq2::results(dds, contrast = list(c(…

RNASeq DESeq2

updated 3.9 years ago • User000

I have analysed the data using three different versions of DESeq2  v.1.10, v.1.14 & v.1.16 values are varying even after using  lfcShrink and betaprior=TRUE while using...I have analysed the data using three different versions of DESeq2  v.1.10, v.1.14 & v.1.16 values are varying even after using  lfcShrink and betaprior=TRUE while using v.1.16.…

rnaseq r deseq2

updated 8.1 years ago • minie

Hi everyone I am trying to use DESeq2 on a Phyloseq object and am running into a consistent error. I've followed all the online tutorials, however whenever...Hi everyone I am trying to use DESeq2 on a Phyloseq object and am running into a consistent error. I've followed all the online tutorials, however whenever I get to the stage to run "phyloseq\_to\_deseq2" I get the following error: …

deseq2 phyloseq

updated 7.4 years ago • amgodogma

I am using DESeq2 to compare gene expression by condition across multiple brain regions. "condition" has 2 levels. "region" has 7 levels...states that "condition_B_vs_A" will return the results describing the effect of condition in the first level of region (so, the effect of condition in region A). This returns many more DEGs than a pairwise Wald test within region...A alone. Is it valid t…

DESeq2

updated 3.7 years ago • EJB

Hi, I am using DESeq2 for DEG analysis in my RNA-Seq experiment. I have 2 bacterial strains: one is the wild type and the other is a mutant (it...Hi, I am using DESeq2 for DEG analysis in my RNA-Seq experiment. I have 2 bacterial strains: one is the wild type and the other is a mutant (it lacks...is the codes: txi.tx <- tximport(files, type = "salmon", txOut = TRUE) …

deseq2

updated 6.7 years ago • alice.checcucci

a list of coefficients for the dependence of gene transcription on the products of other genes and factors, such as d(gene(i))/dt=a(i,j)gene(j)+b(i,j,k)gene(j)gene(k)+...+otherfactors(i) . I'm fairly certain that we don't yet have this level of knowledge...gene(32421)*IntracelluarCalcium] where the positive and negative influences (transcription factors) on a gene's transcription are listed alon…

updated 22.9 years ago • Jeff Sorenson

As the picture describes, I have two DESeq2 objects that have the explanatory variable as either a non-scaled date value, or a scaled date value. For my experiment...As the picture describes, I have two DESeq2 objects that have the explanatory variable as either a non-scaled date value, or a scaled date value. For my experiment these dates are essentially collection dates of wild caught samples a…

dispersionestimates DESeq2

updated 13 months ago • Sam

I am running DiffBind analysis on a ChIP-Seq dataset, comparing Control versus Treatment and using Factor(Donor IDs) as a blocking factor. I want to use the DESeq2 method with dba.analyze, however it gives me an error asking me...to use estimateDispersionsGeneEst instead of estimateDispersionsFit within the DESeq2 model. How do I implement this change through DiffBind? *** ####My code:…

diffbind

updated 7.0 years ago • avantika6194

by DESeq are 1 and I don't know why. I include a minimal working example below. --- library(DESeq2)   \# Toy setting with 1000 genes, 3 groups, and 4 replicates per group.   genes = 1000 groups = 3 replicates = 4   \# Generate...This is a terrible simulation in  \# general, but all I'm trying to do is check my usage of DESeq2.   lambda = r…

deseq2 DESeq2

updated 10.6 years ago • Will Landau

Trying to install DESeq2 in R version 3.2.3 in ubuntu linux 16.04. I follow the instructions of the DESeq2 website: <pre> source("https://bioconductor.org...biocLite.R") biocLite("DESeq2")</pre> at this point if I try to load the library with command library("DESeq2") I get a message that the library can'y be found...which fails due to configuration of RCurl. XML doesn't appear to…

deseq2

updated 9.0 years ago • nkinney06

groups of these patients, in the expression levels of a particular gene (only one). Could I use DESeq2 to do that? The problem is that I can't use a statistical model directly on the raw data, then I would firstly normalize...the raw data of this gene, secondly I want to do a correct statistical test. I thought to use DEseq2 to normalize my gene using all the 150 genes, then do DESeq2 analys…

R deseq2 differential gene expression help

updated 9.5 years ago • fischer87

source using the command line as provided by the website. However when I run the command biocLite("DESeq2") in R it gives the following error: checking for xml2-config... /usr/bin/xml2-config USE\_XML2 = yes SED\_EXTENDED\_ARG: -E Minor...geneplotter’ ERROR: dependencies ‘genefilter’, ‘geneplotter’ are not available for package ‘DESeq2’ \* removing ‘/home/kmh9/Downloads/R-3.2.1/li…

deseq2

updated 8.8 years ago • bekah

Hello Bioconductor and DESeq community. I hope you can help me with this. First of all, I am very new to RNAseq analysis, but I have read a lot and I am very warned that data should not be normalized prior...DESeq2 analysis. However, I am having some concerns with my data. From the beggning. I am analyzing dual RNA-Seq data to study the...and kallisto for those mapped to the de novo transcript…

deseq2 normalization

updated 6.6 years ago • Victor Chano

that different base mean gives different adjusted p-value. I was wondering if base mean is used as a factor for FDR correction for deseq2? Thanks.&nbsp

deseq2

updated 7.2 years ago • Louis Kok

HERVs which were very lowly expressed (see code below).   <pre> pd_nodups$Institution <- factor(pd_nodups$Institution) pd_nodups$Profile <- factor(pd_nodups$Profile, levels = c("Control","Condition")) pd_nodups$Gender...lt;- factor(pd_nodups$Gender) pd_nodups$Age.bins <- factor(pd_nodups$Age.bins) dds <- DESeqDataSetFromMatrix(countData = raw_expr…

deseq2 HERVs low counts prefiltering dispersion estimates

updated 7.1 years ago • rodrigo.duarte88

  Hi, I have questions regarding pairwise comparisons for "both between and within subject" RNA-seq experiments analyzed using DESeq2. My experiment comprises of subjects within block randomly assigned to one of three environmental treatments: 1) CT...pairwise comparisons for "both between and within subject" RNA-seq experiments analyzed using DESeq2. My experiment comprises of subje…

pairwise deseq2 extracting contrasts resultsnames results deseq2

updated 7.1 years ago • Ricardo Rodrigues

Hi, at the moment I am analysing a simple dataset comparing two conditions using DESeq2. For DEG calling i usually go for padjust < 0,05 and foldchage of > 2. I am always wondering whether I should use for that...the shrinked fold change or the fold change deseq2 is giving me straight after the analysis. My code ist pretty straight forward using apeglm for shrinkage. A typical

deseq2

updated 5.2 years ago • ju__ra

am trying to install the DESeq package on the R version 3.2.4 And receive the response "there is no DESeq2 package for R version 3.2.4 As well as I do not succeed to install the latest DESeq2 on R 3.2.1 with the command biocLite...DESeq2)   `` What to do? ``   `` Thanks, ``   `` Mark

deseq2

updated 9.1 years ago • Mark.bogen

Hi, I am using DESeq2 (v1.34) to analyze RNA seq data in r(4.13), but I run into two problems. (1) DESeq2 renames all the genes (2) lack of downregulated...coldata <- read.csv("../Pat2/sample_id_table", sep=",", row.names=1) coldata$Condition <- factor(coldata$Condition) row.names(cts) = cts$gene_id cts <- cts[, 2:7] cts <- as.matrix(cts) all(rownames(colda…

DESeq DESeq2

updated 3.4 years ago • manwar