Bioconductor Forum

I am running DESeq2 v 1.10.1 and I am encountering an error when trying to retrieve information from the the results function.  After...with 10 rows and 1 column       condition        <factor> HumA1      HumA HumA2      HumA HumA3   &…

deseq2

updated 9.6 years ago • tkhodges

Hello fellow DESeq2 users, I am confused about the design of an experiment and how I should implement it when using DESeq2. The experiment...function. This is basically the same as explained in the ?results and is as follows: dds$group <- factor(paste0(dds$stage, dds$condition)) design(dds) <- ~ group dds <- DESeq(dds) resultsNames(dds) res <- results(dds, contra…

deseq2 rnaseq

updated 8.5 years ago • rrcutler

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

Good afternoon, I am aware that this questions is not only relevant to DESeq2 but is more general about Regression Models, but my application right now is in DESeq2. I have design similar to the examples...in the design? Can we exclude the interaction term from the design while maintaining the condition factor and treating the samples as biological replicates using a simplified design? …

deseq2 statistics modelling

updated 6.2 years ago • polyptwo

Hi, I was trying to import the RSEM counts into DESeq2 using DESeqDataSetFromTximport function but for some reason I am getting `Error in txi$counts : $ operator is invalid...is the full code that I was trying to run: > library(tximportData) library(tximport) library(DESeq2) > > dir <- system.file("extdata", package = "tximportData") > list.files(dir) …

deseq2

updated 5.6 years ago • upendrakumar.devisetty

Dear colleagues, Please help me! I was using DESeq2 to analyze gene expression from a batch of IPSCs and have observed some results that I can't explain. The study design...Dear colleagues, Please help me! I was using DESeq2 to analyze gene expression from a batch of IPSCs and have observed some results that I can't explain. The study design was that there were 3 iPSCs derived f…

deseq2

updated 6.9 years ago • W. Gi

default settings (resultsNames(results)) and explore other interactions? For example, here are the 3 factors I am interested in: 1. treatment; levels: disease and control 2. localization; levels: A and B. 3. sex; levels: male and female...in a control? Or DE genes between disease and control for localization A? If I change the order of factors in a design: design2= ~sex + treatment*localization…

updated 11.5 years ago • Mike Miller

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 6.4 years ago • adison.kleinsasser

Hello, I would like to perform a pair analysis in `Deseq2` and I read the vignette and previous questions here but still I'm not sure if my matrix is correct. ```r SampleID Factor Condition...paired samples if coded this way. Ultimately my final model should be the following: `~Replicate+Factor+Condition

DESeq2

updated 4.5 years ago • Alexandre

Hi, I have a design like the one shown below and I want to test whether there are DE genes in condition 1 between Factor A, B and C (multiple comparisons). Is there a way to do this, other than performing all pairwise comparisons, e.g. B.1-A.1, C.1...design like the one shown below and I want to test whether there are DE genes in condition 1 between Factor A, B and C (multiple comparisons). Is t…

deseq2

updated 8.0 years ago • tkapell

formula allows the dataset to run? I am trying to create a design matrix that can be run in DESeq2 and have 8 variables that I am controlling for. The design matrix is as below: ```r dds <- DESeqDataSetFromMatrix(countData...V2) ``` My design matrix is this: ![Design Matrix][1] Column headers are V1, V2.....V9. First column is ID, second column is treatment and the rest are…

DES DESIGN

updated 3.3 years ago • mike

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 8.7 years ago • 247896572

To the developers of DESeq2, First of all, thank you for creating such a great tool! I am currently trying to analyze 16S rRNA gene amplicon sequencing

deseq2

updated 6.1 years ago • microbe

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 5.8 years ago • kajocina2

Hi everyone, Could you guys help me to understand my deseq2 outputs? I used the coding 2x2 design to compare a resistant (R) and susceptible (S) plants. In this intention, we used two...to know, how the controls are being used? Is the test correct the counts of treatments by control first and then compare R and S? Are the results below showing that UP means more expression on S than R and DOWN …

deseq2 2x2

updated 7.5 years ago • filipematias23

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

the following error: <pre> Error: BiocParallel errors element index: 32, 33, 34, 35, 36, 37, ... first error: invalid 'times' value In addition: Warning message: stop worker failed: 'clear_cluster' receive data failed: reached

MBASED biocparallel

updated 7.9 years ago • skhalid7

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

midparent value (for example like [this paper][1]). I was hoping to use modern DE tools such as DESeq2, EdgeR etc. that assume a negative binomial model. What I am confused about is how to incorporate normalization into...parental genes have different lengths, how would I accommodate for this? Suppose I am working with DESeq2 and my parents are A, B and my child is C with parent alleles Ca, Cb. …

DESeq2 limma edgeR DifferentialExpression

updated 23 months ago • pl23

the cell cycle assignments as blocking terms. However, I'm confused about whether to use a blocking factor (the cell cycle assignments) versus a design matrix of covariates (cell cycle assignment scores) in some of the downstream...within the scran package. For example, the modelGeneVar function can take either a blocking factor or a design matrix. Would the blocking factor simply be a character …

scran

updated 6.3 years ago • s1437643

_The Department of Plant Physiology, which is part of Umeå Plant Science Centre, (www.upsc.se), has an open bioinformatics first research engineer position, full-time for one year, with possibility for extension. The working tasks principally are...Physiology, which is part of Umeå Plant Science Centre, (www.upsc.se), has an open bioinformatics first research engineer position, full-time for one …

bioinformatician job next-generation sequencing sweden Job

updated 9.7 years ago • Nicolas Delhomme

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

Hello, I am trying to transform my 16S rRNA count table with rlog for downstream analyses. At the moment I am not particularly interested in continuing with analysing the log-fold change. I have a study design that covers several years, seasons and different sample types (soil, lake, stream, rivers etc). And we sequenced the samples for 16S rRNA DNA and RNA. Together, I have over 250 sample…

deseq2

updated 5.7 years ago • masumistadler

Hi, i did DESeq2 analysis and before i run the DESeq, i did RUVg because i have spike-ins (ERCC) for negative control but i had problem with...dds) keep <- apply(counts(dds),1,function(x) length(x[x>0])>=26) dds<- dds[keep,] dds #factor levels levels(dds$Groups) dds$Groups <- relevel(dds$Groups, ref = "EMM_NEG") levels(dds$Groups) # Identify gene and spike row…

SpikeIn RUVSeq DESeq2 RUV

updated 18 months ago • Ειρήνη

In my OTU data matrix that I would like to input into DESeq2, many of the count values are zeros. I am able to create a DESeqDataSetFromMatrix object from this matrix with the following...In my OTU data matrix that I would like to input into DESeq2, many of the count values are zeros. I am able to create a DESeqDataSetFromMatrix object from this matrix with the following command: dds=DESeqDataSe…

deseq2

updated 10.5 years ago • jport

median absolute residual than my initial run using the parametric fit, and given the same version of DESeq2 being used for both calculations I'm wondering if there is a dependency that got updated somewhere that is causing...this change in how the fit is determined. ``` # Code used to generate DESeq2 output (same in both runs with different results d/t fitType) # Load in the previously produced…

DESeq2

updated 7 weeks ago • colinmccornack

<div class="preformatted"> Dear Community, I am working on the power calculation of a multiple factors design of RNA-Sequencing study. My project has three factors, I use generalized linear model to fit the model including three main effects, two-way interaction terms and the three-way interaction term. The model fitting is implemented by using DESeq and edgeR package. We would like to see…

edgeR DESeq RNASeqPower edgeR DESeq RNASeqPower

updated 11.9 years ago • Guest User

ms; line-height:1.6">I haven't had any problems in the past obtaining a results summary table from DESeq2, where the fit is parametric and all levels are compared between the two conditions.  However, in my most recent...DESeq2 instead has chosen the mean for my most abundant gene's expression level and set this as identical across all samples...ALL of my individuals, which then skews…

deseq2 normalization fitType parametric

updated 9.6 years ago • stwestreich

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 8.8 years ago • glmazzo

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

Hi, I have a block-design for my study where the metadata looks like this: <pre> sample_ID location sex polyp_type age status files 1 INTP_103 proximal 1 1 31 ctrl INTP_1031 2 INTP_103 distal 1 1 31 ctrl INTP_1032 3 INTP_103 rectum 1 1 31 ctrl INTP_1033 4 INTP_105 proximal 2 3 66 disease INTP_1051 5 INTP_…

limma voom

updated 8.7 years ago • jfertaj

I found the source of the error here: groups = colData(rrbs)$group.  This should be groups = factor(colData(rrbs)$group), As the way the groups variable is handled in the filterBySharedRegions.R is it takes the length...of levels(groups) but without taking the factor of this first, levels(colData(rrbs)$group)=null which throws a stop error at line 47-49 even if the intended logic holds

typo manual fix

updated 10.8 years ago • mnaymik

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 8.3 years ago • prab4th

effect of treatment 1 (ctl) versus each of the other treatments. However, once I import my data into Deseq2 file and plot PCA, I can see the samples cluster by biological replicate rather than by treatment (even if I have both...these factors in the degsign), so I wonder if this reflects a batch effect of the experiment itself. I tried using RUVs with k=3 (after...counts and average transcript …

deseq2 ruv batch

updated 6.3 years ago • r.tom

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 5.7 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

must be coercible to non-negative integer In addition: Warning message: In seq_len(ncol(assay)) : first element used of 'length.out' argument</pre> I do not know what it means. I have tried several things: to remove colnames and

singlecellexperiment

updated 7.9 years ago • Marina V.V.

Hi everyone, I've been trying to use DESeq2 to look at expression differences across different gene, with 17 samples across 2 groups. My count data looks as follows...but the following normalization is not. > dds <- DESeq(dds) estimating size factors estimating dispersions gene-wise dispersion estimates mean-dispersion relationship -- note: fitT…

deseq2

updated 6.4 years ago • Charls

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

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 7.7 years ago • sbcn

Hello, guys, I have a problem getting the DEseq2 normalized value. I am using R4.3.2 and DESeq2 version 1.42.0. I have 32 samples for 4 groups. The raw count data is obtained...from Hisat2-string tie pipeline. I would like to get DESeq2 normalized value, but only A1 sample value did not change from the raw count. Could anyone tell me how to resolve this

DESeq2

updated 23 months ago • 史哲

Hello All, I'm something of a neophyte to DESeq2 and want to be sure I'm setting up my analysis appropriately given my sample groups. First, some background: I have a gene

deseq2 experimental design

updated 7.3 years ago • wallace413

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 6.7 years ago • nodice73

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

This is a speedup question like my last, my data is too big to do what I would normally do, I'm doing several TB of data. So my question is how to match two GRangeslist by name and calculate distance between each match( that is, they are from the same transcript) , where the first list contains several ORFs per transcript while cds only have unique rows, namely the first exon. I have already m…

granges distance

updated 8.2 years ago • hauken_heyken

was based upon the labels Sample\#, would the correct design be the following? <pre> Group<-factor(paste(targets$Treat,targets$Time,sep=".")) Patient<-factor(paste(targets$Sample)) design<-model.matrix(~0+Group+Patient...original code used to generate the design matrix in the user guide was as follows. <pre> Group<-factor(paste(targets$Treat,targets$T…

edger anova

updated 10.9 years ago • chwhite

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