Bioconductor Forum

I am doing a differential gene expression (DGE) analysis using DESeq2 v1.24.0 with ~200 bulk RNA-seq samples (whole-blood) with a continuous variable of interest. I am interested in applying...For factors, this functionality is applied by default when calling `DESeq()`. However, based on the [DESeq2 vignette](https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#app…

deseq2

updated 6.2 years ago • bryancquach

Hi, I'm a researcher trying to use DESeq2 for analyzing differential loop for fit-hichip results. I'm curious if I can use it like analyzing differential ChIP...seq using raw contact counts. I gave a try using DESeq2 for differential loop and the MA plot result was non-symmetric. Somebody told me it could be the effect of trended biases...So, I'm trying to correct or remove trended biase…

hichip DESeq2 fithichip differentialloop

updated 4.9 years ago • woongjaej

div class="preformatted">Dear DESeq2 users, Simon Anders, Wolfgang Huber and I have posted a preprint describing the DESeq2 methods to biorxiv: http://biorxiv.org

DESeq2 DESeq2

updated 11.9 years ago • Michael Love

Hi, I am using DESeq2 and after the rld transformation I plotted the PCA and found an interesting result. However, I don't know how to extract...variance are explained by those principal components. Please let me know if this is possible within DESeq2 or if I should use another package. Thanks

deseq2 pca

updated 10.5 years ago • tj.hu

As far as I understand, The process by which DESeq2 models a batch effect is close to : Subtracting the arithmetic mean of the batches' expression values from the genes...on a per-gene basis. Is it possible in DESeq2 instead of modelling only an additive batch effect, to model a multiplicative one as well? For example, divide the expression...nicely. Later, I tried performing differential …

deseq2 batch-effects ComBat

updated 6.2 years ago • Sam

I'm playing around with DESeq2 and I see in the manual that the DESeq() function is a wrapper for estimateSizeFactors(), estimateDispersions() and nbinomWaldTest

deseq2

updated 10.1 years ago • Chris

I have seen peer-reviewed publications where Deseq2 is used for differential abundance analyses of 16s rRNA data. I've recently been informed that Deseq2 may not be appropriate...for analysis of 16s reads. Can anyone provide the evidence-based sources that explain why Deseq2 should not be used for microbiome data and provide any alternatives to hypothesis testing using 16s data in R? Thank

Microbiome 16s Deseq2 16srRNA

updated 3.7 years ago • Katelyn

Hello Michael, I ran DESeq2 to get DEGs between case and control groups. I know that DESeq2 filters lowly expressed genes. So is it possible to get...such as FPKM>1, to define higly expressed genes. I want to get the highly expressed genes from DESeq2 results. Thanks

DESeq2

updated 4.0 years ago • BioEpi

levels, "early", "late", and "untreated". I would like to know how to do a nested comparison in DESeq2 such that I compare ((early Vs untreated) Vs (late Vs untreated)). I've pasted my code below: <pre> samples = read.csv("samples.csv...condition)) #attach the count data to the variable countdata countdata = counts #start DESeq2 library("DESeq2") #construct your DESeq2 data se…

deseq2 rnaseq

updated 10.7 years ago • erin.gill81

Yesterday I managed to install DESeq2 on my home computer but today it simply won't work on my computer at work. I install it using the following command: source...https://bioconductor.org/biocLite.R>") biocLite("DESeq2")   However, when I then use the command library(DESeq2) I get the following: <pre> > library(DESeq2) Loading required

deseq2

updated 8.5 years ago • mdroog

between the single mutants and interaction between the two genes. First I thought that with DESeq2 I can only normalize the counts and extract the normalized counts and do 2-anova afterwards, but as trying to reading...the complete list of your publications I realize that I have to to all with DESeq2, and thus I wanted to confirm the most appropriate design. The programmer used HTSeq before so, I…

deseq2

updated 8.1 years ago • denius

to look at differential gene expression in my study. This is largely based around errors in my DEseq2 code leading to “Error in checkFullRank(modelMatrix)” warnings. I have looked at the manual and multiple comments/forum...5:9),s13=c(4:8),s14=c(5:9),s15=c(4:8),s16=c(5:9),s17=c(4:8),s18=c(5:9))   \#Not real data row.names(d) <- c("clust1","clust2","clust3","clust4","clus…

paired samples deseq2 deseq

updated 8.9 years ago • JamesB

If we look at the example of Deseq2 vignette on interaction terms: <a href="https://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html...interactions">https://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#interactions</a> Table sampleName fileName genotype condition group 1 AI_s1 A1_ATCACG_counts

deseq2

updated 7.0 years ago • salamandra

Running PureCN.R v 1.13.21, I get this warning and these "null device" messages. Are they something to be concerned about? ``` ...snip... INFO [2019-04-29 15:42:06] Fitting variants for purity 0.37, tumor ploidy 3.73 and contamination 0.01. Warning message: In .bcfHeaderAsSimpleList(header) : duplicate keys in header will be forced to unique rownames INFO [2019-04-29 15:42:06] Fitting…

PureCN

updated 6.7 years ago • twtoal

Hello, Can anyone here recommend any posthoc normalisation steps following deseq2 before generating Partial Least Squared Discriminant Analysis (PLSDA) and VIP (Variance of Importance Plots)? I presume...Apologies if this seems like an uneducated question but I'm new to both 'big data' statistics and deseq2

deseq2 normalization posthoc

updated 6.9 years ago • marc.osullivan

to to the number of non-zero parameters such as the Lasso. Is there something akin to this in DESeq2

deseq2

updated 8.2 years ago • kieran.mace

in advance! reads <- as.matrix(read.csv("genereads_ONLY3.txt", sep = '\t', row.names = 1, header = TRUE)) meta <- read.table("metatest2.txt", header = TRUE) mm <- model.matrix(~ stage + treat + stage:treat, data = meta...lt;- subset(dds.interact.results, padj<0.05) dds.interact.DEGs.genes <- …

deseq2 RNA-seq

updated 6.6 years ago • jamesfischer047

span style="font-size:13px">When install DESeq2 to iMac 10.11.6 (R 3.3.1) using the commands   <pre> > source("https://bioconductor.org/biocLite.R") > biocLite...DESeq2")</pre> I receive the following message Warning: unable to access index for repository...downloaded 14.0 MB When lo…

deseq2

updated 8.9 years ago • huzo

or something similar) to prevent this behaviour? [...] data = read.table("counts.matrix", header=T, row.names=1, com='') col_ordering = c(1,2,3,4) rnaseqMatrix = data[,col_ordering] rnaseqMatrix = round(rnaseqMatrix) rnaseqMatrix = rnaseqMatrix...as.data.frame(res[order(res$pvalue),]), file=deseq2_nha_nhc.txt', sep=' ', quote=FALSE, row.names=T) [...] [deseq2_nha_nhc.txt] ba…

PROcess DESeq PROcess DESeq

updated 11.4 years ago • Kuenne, Carsten

Hi, I have a couple of questions about DESeq2: 1) in the DESeq2 workflow, to test the dex treatment effect, the following command was used: dds <- DESeqDataSet(se, design

deseq2

updated 9.8 years ago • tony.fox2016

and compare the FC between the two analyses of some genes. What is the best method to do this using DESeq2? Should I perform two separate analyses with DESeq2 and then compare the FC? Or should I load the four conditions in the

deseq2

updated 8.9 years ago • ribioinfo

population given its cell proportion.  How would you recommend to go about with this using DESeq2?  I had a suggestion to multiply the matrix by the mean of each cellular proportion and run DESeq2 on this new matrix

deseq2 rnaseq

updated 7.6 years ago • cartalop

on RNAseq data, I made my count table using `` kallisto `` and then `` tximport `` to work with `` DESeq2 ``. My genes are a set of cDNAs, (supposed to be corresponding to all the genes of my species), but the annotation is quite bad...B, and not in my cDNA list, I expect to have less reads in A than is B and when the normalization by `` DESeq2 `` occurs, it could create a bias ? Example: A: …

rnaseq deseq2

updated 8.1 years ago • corend

Hi   I'd like to use EDAseq normalized data as input of DESeq2. I found the vignette for DESeq but not for DESeq2. Is there a way to do DESeq2 DEA starting from  EDAseq normalized

deseq2 edaseq

updated 7.6 years ago • zoppoli pietro

Hi Mike, According to the DESeq2 `lfcShrink()` documentation, it appears that the function should work when you provide a `DESeqDataSet` (`dds`) and corresponding...object 'coefAlpha' not found Calls: lfcShrink -> results Backtrace: █ 1. └─DESeq2::lfcShrink(dds = dds, res = res) 2. └─DESeq2::results(dds.shr, name = coefAlpha, lfcThreshold = lfcThreshold) ``` It seems…

deseq2

updated 6.9 years ago • Michael Steinbaugh

Hello, I would like to inquire about using DESeq2 package in order to compare different types of read data: 1. Would it be OK to use DESeq2 to compare read data between homologous...Hello, I would like to inquire about using DESeq2 package in order to compare different types of read data: 1. Would it be OK to use DESeq2 to compare read data between homologous genes __in different…

deseq2

updated 7.9 years ago • yair.gatt

bioc/src/contrib/DESeq2_1.34.0.tar.gz" #install.packages(url, repos=NULL, type="source") library(DESeq2) packageVersion("DESeq2") # Set up the conditions based on the experimental setup. cond_1 = rep("cond1", 2) cond_2 = rep("cond2", 2...the data from the standard input. countData = read.table("counts_bad.tsv", header=TRUE, sep="\t", row.names=1 ) # Build the dataframe from the condit…

DESeq2

updated 4.0 years ago • Andrey

read nanopore data? Is there some option I can activate to get our long reads to work better with DESeq2 (or any other tool)? My core problem is that the Log2FC values reported by DESeq2 do not reflect values I calculate myself...an unadjusted fold change value. In extreme cases, there's a log difference of about 4 (i.e. DESeq2 is reporting a Log2FC value of 8, whereas I calculate it as abo…

deseq2 nanopore

updated 6.6 years ago • David Eccles (gringer)

nbsp; The structure of my dataset is 4 cell lines of 2 genotype with biological duplicates (4\*2\*2 samples), the purpose of the analysis to assess the effect of different genotypes (KO vs WT) on the gene expression

rnaseq deseq2

updated 8.9 years ago • JunLVI

Hello, I am new to RNA-seq. I have output from `tximport` and I want to use `DESeq2`. I have used five replicates for each of two treatments and I want to check the difference. I am not sure which design...Hello, I am new to RNA-seq. I have output from `tximport` and I want to use `DESeq2`. I have used five replicates for each of two treatments and I want to check the difference. I am not s…

deseq2

updated 5.8 years ago • zen

all treated vs all controls samples (I mean I do not want DE for each experiment separately).   DESeq2 is a right choice for my goal? actually I saw its tutorial but the explanation is for one experiment how can I use

deseq2

updated 9.0 years ago • elhamdallalbashi

Hi, I am using DeSeq2 for a set of metatranscriptome data for which I also do have estimations for the number of total transcripts per L...Hi, I am using DeSeq2 for a set of metatranscriptome data for which I also do have estimations for the number of total transcripts per L within...on absolute instead of relative expression data. My idea was to multiply the automatically generated DeSeq2 size…

deseq2

updated 9.1 years ago • sara.beier

Hello, I'm developping package with DESeq2 and agricolae as dependencies. But DESeq() function seems to not work anymore when package agricolae is called. ``` library...agricolae) library(DESeq2) ## DESeq() Example commands cnts <- matrix(rnbinom(n=1000, mu=100, size=1/0.5), ncol=10) cond <- factor(rep(1:2, each=5)) # object construction

deseq2 dependendies conflict agricolae

updated 5.7 years ago • etienne.rifa

Hello,   I have a question about the best DESeq2 experimental design matrix for my dataset.   I am working with 75 RNAseq samples from the same tissue, but classified...subtype:stage </pre> (apologies if the syntax is wrong!) My second question is regarding how DESeq2 handles data not included in the analysis. As I said above, we have 75 samples, but right now I'm fo…

rnaseq deseq2 design and contrast matrix

updated 10.9 years ago • m.fletcher

Hello, I’m working with Deseq2 in order to analyse some RNA-seq generated with a plant species. I have a time series experiment with 8 time point and...Hello, I’m working with Deseq2 in order to analyse some RNA-seq generated with a plant species. I have a time series experiment with 8 time point and 4 replicates for each time point.   I just have a question concerning the normalisat…

deseq2

updated 7.3 years ago • Alex So

Dear Micheal, We are want to use DESeq2 using gene specific covariates (i.e. a separate set of covariates for each gene; these are also count data with the identical...this. We thought that you might have an idea? Kind regards, Christian edit: to DESeq2

deseq2

updated 9.8 years ago • c.oertlin

script. However, these counts are not integers, is there a way I could use this matrix in Deseq2 or I will have to generate it again using a method from the Deseq2 manual? Thanks, Catalina &nbsp

deseq2

updated 7.9 years ago • Catalina Aguilar Hurtado

Hello All, for estimating the differential expression values,what statistical test does DEseq2 use for estimating the differential expression values,is it t-test, Fisher exact test or some other

deseq2 statistics

updated 8.9 years ago • elhamdallalbashi

1.6 fold change higher in OAC wBE than normal mucosa. ![DESEQ2 result shows OAC_wBE has higher expression than Normal Muc][1] But when I plot them into a box plot, it shows that the normal...of mean between the two groups, the result is similar with the log2foldchange result generated by DEseq2. However, when I plot it, the mean (shown in hexagonal white box) is higher in normal mucosa than OA…

DESeq2

updated 4.6 years ago • Chloe

all, I have RNAseq data of two groups. After doing differential gene expression using edgeR and DESeq2(the results are similar). I found the distribution of logFC is a little strange, having two peaks in the distribution...Code can be seen bolow: <pre> P1<-read.table("P1.STAR-counts-stranded.txt",header = TRUE) row.names(P1) <- P1[,1] P2<-read.table("P2.STAR-counts…

edger deseq2 rnaseq differential gene expression

updated 8.1 years ago • Jack

div class="preformatted">Hi, We recently upgraded to DESeq2, and we are trying to figure out the differences. We couldn't find an explanation in the documentation regarding the...with count 0 in a specific gene, we get a basemean of 0 in DESeq, and a basemean of 0.68586719 in DESeq2. I understand how the calculation is done in DESeq, but not in DESeq2. Can you explain please? Thanks -- outpu…

DESeq DESeq2 DESeq DESeq2

updated 11.5 years ago • Guest User

A couple of weeks or months ago, a question was posted regarding DESeq2's behavior when dealing with samples with one extreme outlier. In that case, DESeq2 identified that gene as DE, although...there was only 1 out of N samples with extreme counts. Michael Love suggested a way to force DESeq2 to look at all replicates. I've been searching for the post for a while using both Google and the foru…

deseq2 outliers

updated 8.0 years ago • paul.alto

on how to use arrayQualityMetrics to identify sample outliers with DESeq data sets produced using DESeq2?  I'm having trouble generating a file that the "arrayQualityMetrics" function will accept using DESeq2 functions...for function ‘platformspecific’ for signature ‘"SummarizedExperiment""... the standard output of the DESeq2 functions I'm calling. My current work-around is to use DESe…

arrayqualitymetrics deseq2 sample outliers

updated 10.9 years ago • rachelwright8

instead just keep the Dseq(dds) portion? ``` Counts <- read.csv("1_raw_data.csv", header = TRUE, row.names = 1, sep = ",") Counts condition <- factor (c("S","S","S","C","C","C")) coldata <- data.frame (row.names = colnames(Counts), condition) coldata

Dseq2 RNASeqData apeglm

updated 16 months ago • Gordon

Since looking at the row variance and DESeq2 both act as ranking mechanisms for genes, is there any sense to taking the top 1000 or 5000 genes with the highest variance...across samples from an RNA sequenced set and running the DESeq2 pipeline on that subset to look for differential genes between groups (so simple design ~condition)? Thanks!&nbsp

deseq2 variance genes

updated 8.1 years ago • hs.lansdell

Hello, I want to generate a dummy sample data but I want to do it based on DESeq2 result. Suppose, I have a gene, gene A and I have do DESeq2 analysis between cancer and normal. The result is, gene A logFold...fold change with 0.01 p-value. Is it possible to do that? I imagine something like this. Because DESeq2 use negative binomial as distribution, I just need to make  random sampl…

deseq2

updated 9.8 years ago • bharata1803

replicates per covariate combination (so 8 samples total, n=2 per cell) that we are analysing using DESeq2. Normally DESeq2 generates a Cook's distance for each replicate within a cell (by "cell" I mean unique combination of covariates...individual observation with the high Cook's distance, but we are not aiming for this.) I see that DESeq2 still generates Cook's distances when n=2, and these…

deseq2

updated 6.5 years ago • stuart

Hi, When converting a GInteractions object into a dataframe, a ‘duplicate row.names’ error is generated. This is presumably a problem with the as.data.frame function, which encounters...gt; as.data.frame(GInt) Error in data.frame(seqnames = as.factor(seqnames(x)), start = start(x), : duplicate row.names: name_1, name_2, name_3, name_4 > GInt <- GInteractions(unname(Gran…

InteractionSet

updated 4.5 years ago • noa

i.ibb.co/NCJCD0s/Screenshot-from-2019-03-10-15-10-00.png"/></a> coldata <- data.frame(row.names=colnames(countdata),genotype,Rep,stimulation,batch) coldata$group<- factor(paste0(coldata$stimulation,"_",coldata

deseq2

updated 6.8 years ago • Gyan Prakash Mishra

sample (and replicate), do I have to convert zero read counts to ones (pseudo counts) while running deseq2? I assume I don’t have to, but a quick clarification.</span

deseq2

updated 11.1 years ago • Prasad Siddavatam

 Hi all, I am using variance stabilizing transformation on my rna seq count data with Deseq2. Do I need to use quantile normalize the samples or does variance stabilizing transformation function take care of...nbsp;Hi all, I am using variance stabilizing transformation on my rna seq count data with Deseq2. Do I need to use quantile normalize the samples or does variance stabilizing t…

quantile normalization deseq2

updated 8.2 years ago • lirongrossmann

Hi all, Regarding the package DESeq2, -What are the input files? BAM/SAM files? -Does it makes the counting and the differential expression analysis, or just

deseq2 differential gene expression rna-seq

updated 9.7 years ago • cirisarri95

Hello, I am using DESeq2 on a project, where I tested various extraction volumes and types and got amplicon data out. So for instance, I have two...tested, but I was going to set up different experiments for them and just pull out one site set up deseq2 and then do the other experiment. A few other issues I am having, my Volume is being treated as numeric, even when I turned

deseq2 Tutorial

updated 5.6 years ago • Anna.bramucci

Hi Michael, I have a couple of questions about DESeq2. 1) Could we use it for repeated measured outcome? Do we only need to add a time variable in the design as below? dds <- DESeqDataSetFromMatrix...outcome here? Or we can only use the factor variable for condition due to NB distribution behind the DESeq2? 3) I saw you mentioned that DESeq2 only works for replicates data, here…

DESeq2

updated 4.5 years ago • lovelymaoqin

me " There are samples duplicated. We will not be able to prepare it" How do I get rid of the duplicate files? My code and session ``` > library(TCGAbiolinks) > library(xlsx) > library(DT) > library(edgeR) > library(org.Hs.eg.db

TCGAbiolinks

updated 4.1 years ago • raf4

I'm trying to reinstall DESeq2 with R 4.2.2. I used ```r if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("DESeq2

DESeq2 SummarizedExperiment DelayedArray

updated 2.9 years ago • Danielle

At some point DESeq2 was updated so that LFC shrinkage was no longer performed automatically, and that functionality was moved into a...At some point DESeq2 was updated so that LFC shrinkage was no longer performed automatically, and that functionality was moved into a separate...in some samples and they have very high variance, and I decide to remove them prior to running DESeq2. I think the es…

deseq2

updated 5.2 years ago • www1124

the RNA\_seq dataset which containing tumor and normal tissue to find differently expressed genes by DESeq2::DESeq. Second, because i only want to normalize the tumor data, so i use DESeq2::rolg to transform the data only containing...data which containing the tumor and normal tissue, and set the tumor to some groups, and use DESeq2::DESeq to do differently analysis.  Here is my questi…

deseq2 rna-seq

updated 7.5 years ago • 137737756

Hi, I am doing differential expression analyses for the first time and using DESeq2. The tutorials are great, but I have a couple niche questions that I cannot find the precise answer to. 1) If I use a truth...Hi, I am doing differential expression analyses for the first time and using DESeq2. The tutorials are great, but I have a couple niche questions that I cannot find the precise answer to…

deseq2

updated 7.9 years ago • jrlarsen

the effect of three treatments (8 animals/treatment) on the metagenome level and Now I want to use DESeq2 tool to find the specific genes that are significantly affected by treatment per gut section. For example Effect...of treatment, A compared to Treatment B in Ileum.  Therefore, I used DESeq2 with the following design:  <pre> <code>dds$group <- …

deseq2 metagenome

updated 8.3 years ago • ghanbari.msc