Bioconductor Forum

Dear DESeq2 community, I am currently working with RNA-seq data from pre- and post-treatment samples from 3 patients across 4 different...build 1 DESeq model using all of these samples, or to use each of 4 cell types to build 4 separate DESeq2 models? I am aware of vignette section titled "If I have multiple groups, should I run all together or split into pairs...expressed genes for cell type …

deseq2

updated 5.7 years ago • d93espinoza

Hej I have a question concerning the use of interaction designs with DESeq2. My experimental design looks like this: 3 treatments: control, low, high 4 sampling time points throughout a years season...Hej I have a question concerning the use of interaction designs with DESeq2. My experimental design looks like this: 3 treatments: control, low, high 4 sampling time points throughout a year…

deseq2

updated 10.0 years ago • juliah

Hi, I have a DESeq2 script that used to work until recently, I'm not sure if I updated a package which suddenly caused it to stop function...and I'm hoping to get some insight on what the issue might be stemming from. colData has 6 factors (A,B,C,D,E,F) ``` dds <- DESeqDataSetFromMatrix(countData = countData, colData = colData, design = ~ Experiment) dds <- DESeq(dds

DESeq2

updated 2.2 years ago • J_Can

Hi DESeq2 Community, I have a bulk RNA-seq dataset consisting of four groups: each group has an n=4 and is genetically identical...genes with high variability due to stochasticity/noise. My approach involves: 1. Using DESeq2 for differential expression (DE) analysis with each group as the reference: ```r reference_groups <- c("PRENATAL_A", "PRENATAL_B...if it is differentiall…

DESeq2

updated 16 months ago • DL

<div class="preformatted">Hi, I just compared the same dataset using DESeq 1 and DESeq 2. Strikingly, while the baseMeans are the same for the same gene, the log2FoldChange is actually different!? There must be an error in the R script I am using or how can that difference be explained? DESEQ1 id baseMean baseMeanA baseMeanB foldChange log2FoldChange pval padj "real" log2FC comp…

DESeq DESeq

updated 11.4 years ago • Kuenne, Carsten

Hello! Me and some colleagues are trying to work out if we need to account for multiple testing when using DESEQ2 or if this is something the package covers already. And also, how to handle global testing rather than pairwise. **Our data...Me and some colleagues are trying to work out if we need to account for multiple testing when using DESEQ2 or if this is something the package covers already…

MultipleComparison DESeq2 Genetics contrasts RNASeq

updated 2.5 years ago • a26fd14e

div class="preformatted"> Hi! I am currently programming a function for easy use of DESeq2. I would like to export my graphs with the pdf() command. It works fine for the dispersion graph and other volcano plots...that I programmed, but I encountered some problems with the plotPCA() function. First I have to execute it at the very end of the function to see the graph, and the if I use pdf()..…

graph DESeq2 graph DESeq2

updated 11.9 years ago • Guest User

match it with a dataframe in a downstream analysis. However, if I change the GENEID all of a sudden DESeq2 says I have 30200 genes rather than 25900. I thought tximport only is matching the transcript IDs between the gtf file...tx2gene <- df[, 2:1] head(tx2gene) #should have 2 columns with transcript ID as the first column #because the ".v2.1" won't match with the other file, I n…

deseq2 tximport salmon

updated 5.9 years ago • gmchaput

strategy is better in DESeq2.  To me, the first strategy makes more sense than the second one.  Could you help me to choose better analysis way...using DESeq2?  Also, we found logfc of many genes in DESeq2 analysis results are different from logfc we manually calculated...from RPKMs normalized by DESeq2.  I guess this is because DESeq2 reports estimated logfc. …

deseq2 data handling comparing more than two groups normalization logfc

updated 10.1 years ago • bioboy

Hello, I am attempting a new DESeq2 install on my new computer and I am running into a problem installing the "GenomeInfoDbData" package from BiocManager...Error: ERROR: no packages specified In R CMD INSTALL My User folder has a space between my first and last name and the package can't seem to work around that. This has not been a problem when installing any other packages

genomeinfodbdata

updated 6.8 years ago • hdwhitti

Hello All, I am trying to run DE analysis using DESeq2 and wanted to know what would be a better/correct design matrix for my analysis. I have two disease condition A and B...Hello All, I am trying to run DE analysis using DESeq2 and wanted to know what would be a better/correct design matrix for my analysis. I have two disease condition A and B. Cells

deseq2 deseq

updated 8.1 years ago • hrishi27n

ve read myself into a stand-still regarding how to best optimize the different variables within the DESEq2 package for my particular data. I really want to better understand the details of how Deseq2 processed my counts My...colData <- read.csv("subject_metadata_deseq2.csv", row.names=NULL, fill=TRUE) # now make this a factor as it will be the variable we will use define groups for the…

DESeq2 RNASeq

updated 3.3 years ago • marinawakidanna

differential abundance analysis on some metagenomic data. In comparing the results of edgeR and DESeq2, I find that there are drastically more differentially abundant tags found by DESeq2 compared to edgeR (n=59 vs. 17, both...FDR < 0.05). Further, only 10 out of 17 of edgeR's significant tags overlap with those found by DESeq2. Does anyone know why such a discrepancy would occur? (Update…

edger deseq2 differential expression

updated 8.0 years ago • audrey.o.renson

nbsp; Dear community,  I am having troubles with the DESeq2 analysis of time course experiments and was thinking someone could point me to the right direction.  I have 3 different...white-space: pre-wrap;">here </a><span style="white-space:pre-wrap">(in the time course section), DESeq2 throws an error</span>   "..the model matrix is not full ran…

deseq2 multiple time points R

updated 8.8 years ago • Dmitry

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 8.5 years ago • tangming2005

Hey everyone, I know the `plotPCA` function from `DESeq2`uses, by default, only the 500 most variable genes. I was wondering if it makes sense, or if anyone has done, a plot where...Hey everyone, I know the `plotPCA` function from `DESeq2`uses, by default, only the 500 most variable genes. I was wondering if it makes sense, or if anyone has done, a plot where we...be824406 Where X is the…

DESeq2

updated 21 months ago • andrebolerbarros

do this I was just wondering if there is a quicker/cleaner way to run through all my comparisons in DeSeq2.  Like the question pasted above, I want to compare all my genotypes (12 genotypes) for my treatment (disease exposed...I am therefore joining the two factors and using contrast to analyse these. This obviously will require a large number of contrasts to be made for all the...genot…

deseq2 DeSeq2

updated 7.2 years ago • bdy8

Hi, all/Micheal Love,   Is there a way in DESeq2 package to hep with this kind of problems? For example, I may be able to think of tens of possible variables that may affect...a robust estimation?   From the literature, I saw someone using the PC1 as the corresponding factor. Then ANOVA model could be applied to testing the contribution of each possible variables to PC1. This …

deseq2 rnaseq

updated 7.1 years ago • Raymond

Hi, Although I have read the extensive information of the DESeq2 vignette and several comments onf forums, I am unable to create a design formula without getting the error *the model...Posterior at each stage and across stages. My clustering analysis shows that the main clustering factor is being from the same egg. If I use the limma "removebatcheffect()" I can get read of this effect, but …

deseq2

updated 6.6 years ago • Ysland

Hi, I need help the analysis of my RNA-seq samples using DESeq2. This is the first time I am doing this kind of analysis. So, I need some help with my data. I have gotten some results but I...KD_treated_4-2 siX hormonetreated Q</pre> I have 2 questions regarding the analysis with DESeq2. 1: I would like to find differentially expressed genes in KD\_treated compared with Ctr\_t…

deseq2 rnaseq R

updated 8.7 years ago • zeynep.nenseth

term versus grouping with different betaPrior arguments using version 1\_14\_1. I'm still using DESEq2\_1.14.1. I've been working on differential expression analysis of drought-tolerance in rice. I have 2 genotypes...colData(dds)$condition<-relevel(colData(dds)$condition, ref = "Control") dds$group<-factor(paste0(dds$genotype, dds$condition)) design(dds) <- ~group…

deseq2 interaction term multiple groups betaprior

updated 7.6 years ago • tarun2

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 2.8 years ago • suphamon.j

Hi, I am doing DE analysis. I have 4 conditions: control, drug1, drug2, drug3 (2 replicates for each condition). I started with Salmon to count transcripts and imported them with tximport. After this I constructed DESeq data set using DESeqDataSetFromTximport following this [tutorial](https://bioconductor.org/packages/release/bioc/vignettes/tximport/inst/doc/tximport.html#deseq2). Then I tried…

deseq2 salmon

updated 6.6 years ago • chipolino

You have explanined the pasila package but how will it be when I have two plain text files, where first column contains ensembl ids and second column contains counts? I have no solid R background and your help would be appreciated...sampleTable=sampleTable, directory=directory, design=~condition) colData(ddsHTSeq)$condition<-factor(colData(ddsHTSeq)$condition, levels=c("Untreated", "Treate…

updated 12.6 years ago • Kisun Pokharel

<div class="preformatted">Hi Mike, I would like to try DESeq2 package now. My project has three factors: A with 16 levels, B with 2 levels and C with 3 levels, in total I have 16 x 3 x 2 = 96 groups, for each group, we have 8 biological replicates in our original experiment design, which ends up with 96 x 8 =768 biosamples. I can't understand why we can't estimate any interaction terms i…

DESeq DESeq2 DESeq DESeq2

updated 11.4 years ago • Yanzhu Lin

Hi, I am trying to run DESeq2 with the duplicated raw counts from 4 groups and 2 conditions using the  two-way ANOVA design below. Referring...Hi, I am trying to run DESeq2 with the duplicated raw counts from 4 groups and 2 conditions using the  two-way ANOVA design below. Referring a...vignette of DESeq2, various comparisons have been run as below. Besides of these results, I…

deseq2 results

updated 10.4 years ago • jjinhyoungkim

I am trying to set my dds size factors as the ReadCount as explained in https://github.com/t-neumann/slamdunk/issues/70. However, I took the read counts from

DESeq2 sizefactor

updated 2.9 years ago • La

Hi, In the DESeq2 vignette, it is stated specifically that the `name` and `contrast` argument in `results()` can be used to build equivalent...results tables (http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#differential-expression-analysis). I found this in general to be true, **with one exception**. I think...3 samples per condition: ``` # output: DataF…

deseq2

updated 6.5 years ago • Vincent de Bakker

do I prevent the error from occuring? Is it ok to use stringsAsFactors=FALSE ? What is meant by factors? > setwd("C:/Users/mlinan/Counts") > samples=data.frame(condition=c(rep("Two", 2), rep("Four", 2)), + row.names=dir(path="C:/Users/mlinan...file.path("C:/Users/mlinan/Desktop/Counts", "My_file.gff")) *Error: all(unlist(lapply(design, class)) == "factor") is not TRUE* * * &…

DEXSeq DEXSeq

updated 12.6 years ago • Bio152

Hi there, I'm working on a metatranscriptomics project and want to perform DEA using DESeq2. I am however not sure how to insert my design. The sample set-up is as follows: There are 3 plots on dry, 3 on wet ground. From...Hi there, I'm working on a metatranscriptomics project and want to perform DEA using DESeq2. I am however not sure how to insert my design. The sample set-up …

Transcriptomics DESeq2

updated 4.8 years ago • seppe.demits

transcripts from an experimental time point versus a control time point. However, whenever I run DESeq2 on the counts table, it throws this error: estimating size factors estimating dispersions Error in checkForExperimentalReplicates

DESeq2

updated 6.8 years ago • csteely4

Hi there, I am trying to use limma for some rna seq data and model subjects as a random effect as I have paired samples. I have already done analysis in DESeq2 and got 400 (up and down) significant DGEs. When repeating in limma I only get 19 DGEs. I'm not sure where I am going wrong in...data and model subjects as a random effect as I have paired samples. I have already done analysis in DESeq2…

limma RNASeq R

updated 3.6 years ago • Beth_b

I am executing the deseq2 for two conditions sick and healthy. Each condition has 4 cell types defined as group (a1, b1, c1 and d1, a2, b2, c2, d2). each group...2 sick c1 8 healthy c2 31 healthy b2 9 healthy d2 my code is: ``` > metadata_sorted$Group <- factor(metadata_sorted$Group) > metadata_sorted$Condition <- factor(metadata_sorted$Condition) > col_data_s…

DESeq2 Designmatrix limma

updated 18 months ago • Neha

nbsp; I have the following error while trying to install DESeq2 from bioconductor.  How do you fixeed this?     source('http://bioconductor.org/biocLite.R') Bioconductor...3.3 (BiocInstaller 1.22.3), ?biocLite for help > biocLite('DESeq2') BioC\_mirror: https://bioconductor.org Using Bioconductor 3.3 (BiocInstaller 1.22.3), R 3.3.1 (2016-06-21). …

deseq2

updated 9.2 years ago • tran_tim

total number of mapped reads.", which would suggest 900,000 in your example. > The normalization factor I calculate is like 0.5,1.5,1.3 ,but in you manual they are all near to 1. > Is it right?? It is more extreme than I normally...plot. Perhaps you should look at one of those for your data and assess whether the normalization factors are appropriate. Best, Mark > ???? M…

Normalization edgeR DESeq Normalization edgeR DESeq

updated 13.7 years ago • Mark Robinson

Hi - I am using DESEq2 to analyze a dataset with two factors, each with two levels. I am therefore using a standard model matrix, with the following...is not the equivalent numeric contrast, what is? Thank you in advance for your help. This is my first support forum post, so please excuse me for leaving anything out!   <pre> > sessionInfo() R version 3.2.1 (2015-06-18)…

deseq2

updated 10.2 years ago • ryan.mcminds

found in the DNA. So, overall the design looks like this. I named pre treatment "before" so that DESeq2 will automatically take it as the first level in the factor. All three groups are of interest to compare to the other...individual (Patient), I would run like so (maybe afterward also re-running with group1 not as the first level so can test that): <pre> dds <- DESeq(DESeqDataSet…

deseq2

updated 8.3 years ago • hmgeiger

Hi, I am treating some RNASeq data whose experimental design includes three factors. I am interested, at first, in retrieving those genes showing the triple interaction, using voom + lmFit. I’ve read several...Hi, I am treating some RNASeq data whose experimental design includes three factors. I am interested, at first, in retrieving those genes showing the triple interaction, using voom + lmFi…

RNASeq limma voom anova

updated 8.5 years ago • David Rengel

Hello everyone/ RECOUNT3/ DEseq2, Before i raise this question, i kind of read some previous post (https://support.bioconductor.org/p/9143498/) about DEseq2...my question is is it possible and how to combine 2 rse objects download from Recount3 and perform DEseq2 analysis on 2 different datasets, for example, between cancer and GTEx normal tissue? Also, if it is possible, how can...tell/ what …

DESeq2 recount GTEx TCGA recount3

updated 2.7 years ago • David

1. In Diffbind package, I want to block multiple factors, e.g. Tissue, condition and factor. In the Vignette, there's example for blocking only one category, not all 2 or 3 together...How can it be done? Thank you very much in advance! 2. Also, I tried to block using multiple factor like this: > ` > > `"block=c(DBA_CONDITION,DBA_TISSUE, DBA_FACTOR)"` Is it the …

diffbind rory stark chip seq

updated 5.1 years ago • bioinfouser2

Hello Mike, please kindly advise on the following question regarding analysis with deseq2. This might be a very general inquiry about running deseq2 with a continuous variable, but the characteristic of this...I'm considering my variable as continuous, but I'm not sure if I'm conducting this correctly within DESeq2. Below is part of my coldata: ``` > coldata Age Sex N1864 1…

deseq2

updated 5.7 years ago • jasminelee0603

I am using DESeq2 to normalize data for some microbiome and eDNA metabarcoding projects. My datasets are observational/ecological...and there are many factors that I am interested in assessing with downstream analyses. For example, with my microbiome dataset, I am interested...sexes, age groups, reproductive status, and season of certain wildlife species. When running DESeq2, should I incorpo…

DESeq2 des

updated 3.1 years ago • Devin

Hi dear list, I'm trying to use a package to perform some analysis but I need to process a file first of all. I have file A with 6 columns and 443816 rows and I need to select from here the rows where the string in the first column...in file B that has 333751 rows and only one column. So all the strings in file B are present in the first column of file A but the contrary is not true. I'm kind of…

updated 16.9 years ago • Laura Rodriguez Murillo

that I was wondering if I could to some kind of filtering of the DGEList-object. My sample names are factors in "y_keep[["samples"]][["group"]]" But because it is a factor all my trials to sort them were unsuccessful.... Could you help me with

edger

updated 5.2 years ago • dojo89

<div class="preformatted">Fernando, Capitalize the "b" in the "Batch" header, and let me know if this works. Alternatively, use the ComBat from the sva package of bioconductor. This will be less finicky. Evan On Jun 4, 2013, at 11:12 AM, Fernando Andrade wrote: > Hi there, > > This is the first time using combat, and i'm using it on a very large set of data built up…

probe sva probe sva

updated 12.6 years ago • W. Evan Johnson

hello, I am working on DEseQ2 to find the differentially expressed when i compare the control (3 replicates) Vs. 2 treated samples (3 replicates each...when i compare the two treatments to the control. But im not sure how to set up an experiment in Deseq2               …

rnaseq degseq

updated 8.2 years ago • laksharikrish

I want to check contrasts between certain samples in my dataset, and I was told that for DESeq2 we need to use raw data that is normalized. I don't have real data to practice this on but I have been going through the...I want to check contrasts between certain samples in my dataset, and I was told that for DESeq2 we need to use raw data that is normalized. I don't have real data to practice this …

DESeq2

updated 14 months ago • Katherine

I trying to add some interactions to my DESeq2 design matrix. My 12 samples are divided into two batches. There are two strains. These samples are coming from 6 individuals...strainB","strainB","strainB","strainB","strainB","strainB") animals <- factor(rep(1:6,each=2)) ind.n <- factor(rep(rep(1:3,each=2),2)) …

DESeq2

updated 2.4 years ago • lamia11me

Hello,  I have a question about the design of a DESeq2 experiment analysing RNA seq data. I have 3 factors to take into account: condition, patient and cell type. I have 2 conditions...td>4</td> <td>B</td> </tr> </tbody> </table> After reading the vignette, I tried creating a nested factor for the patient, giving the following: <table border="…

deseq2 multiple factor design nested design interaction term

updated 8.6 years ago • zahra.aboukhalil

Hello how are you? I reopen this question because the following has happened: I am doing a differential expression exercise using the hisat2, stringie & DESeq2 workflow. Finally I use the python prepDE.py script recommended in the StringTie manual to extract the counts. So far...has happened: I am doing a differential expression exercise using the hisat2, stringie & DE…

pvalue NA R DESeq2

updated 4.1 years ago • JOHAN HERNANDO

for us at the Community of Bioinformatics Software Developers (CDSB in Spanish). Today we had our first Bioconductor package submission. Here's the annoucement from Twitter. I would also like to thank Martin Morgan and...S Carvalho for going to Mexico in 2018 to help teach the first of our CDSB workshops, as well as everyone who has helped us along the way. Best, Leo --- <img src="h…

CDSB News

updated 5.8 years ago • Leonardo Collado Torres

Hello, I am running DESeq2 with this metadata table - | Condition | Time | Batch | |-----------|------|-------| | Control | 0h | 1 | | Control | 12h | 1 | | Control | 24h | 1 | | Control | 0h | 2 | | Control | 12h | 2 | | Control...it says "the model matrix is not full rank" I looked at other posts and tried the solution under DESeq2 manual - Levels withou…

DESeq2

updated 12 months ago • bhandary.8590

Hi,  I've got some data that comes under an unusual design and I was looking for some advice. The experiment consists of 3 time points, 3 conditions, in triplicate, and it's paired by treatment. Design Matrix <pre> > design Pairing Treatment TimePoint 1 A type1 2hr 2 A type2 2hr 3 A type3 2hr 4 B type1 …

deseq2

updated 10.4 years ago • andrew.j.skelton73

Hello, i'am a bit new to deseq2 and wanted to understand I wanted to test for two factors (meiosis stage and température) separately: > code samples...lt;- na.omit(res_dds_padj) summary(res_dds_padj) > Summary (Meiosis Stage factor) out of 124677 with nonzero total read count adjusted p-value < 0.05 LFC > 0 (up) :…

DESeq2

updated 4.6 years ago • Mohamed Malek

Hi I am wondering which way could allow me to retrieve the first exons from genome with the information of the exon length. the purpose is to retrieve the first exons for gRNA design

annotation

updated 6.1 years ago • XIN1988

Hi, I am trying to analyze my 16S data using DESeq2, and I would like some advice on the correct formula I should use. I have before/after data for two different treatments

deseq2 16s microbiome

updated 5.9 years ago • mstagliamonte

Hi, I used DEseq2 for estimation of differentially gene expression in iPS cells and CMs cells my design was first sample_name cell_type

DESe DESeq2

updated 4.2 years ago • Dinesh

Hi BioC community, I work on metagenomic data (16S sequencing) and I want to indentify microorganisms differentially abundant between two groups. With this aim, I use the size Factors computed with GMPR, a normalization method adapted to metagenomic data. Consequently,I can not use directly the DESeq...indentify microorganisms differentially abundant between two groups. With this aim, I us…

DESeq2

updated 4.8 years ago • eleonoregravier

Hello!  I'm trying to figure out which design model is correct for my human RNA seq data. I have outcome data, here 'condition' that when examined alone, returns no differentially expressed genes (as design=~condition). So digging around led me to believe I need to control for the sex of the samples. I tried both of the below, and am unsure which is accurate...  <pre> d…

deseq2 differential gene expression

updated 8.1 years ago • hs.lansdell

Hi, I'm using DESeq2 on 3 high sugar genotypes and 3 low sugar genotypes. None of the genotypes or sugar groups are reference, but DESeq2 considers...genotype), and found DEGs. I was wondering if what I did, regarding the reference assumption by DESeq2 and my contrasts, is correct, and if it is not, what do I need to do? Thank you

deseq2 contrast

updated 5.2 years ago • bahmanik@msu.edu