Bioconductor Forum

Hello, Me and a colleague are performing differential expression analysis on a dataset comprised of 2 groups, controls and cases. We wanted to test/correct for batch effect so we decided to use SVA and we were obtaining the initial files from a shared folder.  We were however getting different results. We thought it might be due to small differences in our scripts, however, w…

deseq2 version compatibility

updated 8.6 years ago • dmffrancisco91

Hello, I would like to use DESeq2 to identify peaks in ChIP-seq or CLIP-seq for given regions. As I have specific regions, I want to use DESeq2 instead of...IP(pulldown) and want to compare them to identify enriched regions. In the case, can I use default DESeq2 pipeline similar as DiffBind ? Or Do I need to use one-sided test for enriched regions ? As I understand, if I want to check

deseq2 diffbind

updated 5.7 years ago • bioinfo

Hi everyone,   We have tried many times to install DESeq2 to our local instance of Galaxy. The install is successful but when we run the tool we get the following error:   <pre...is no package called ‘getopt’</pre>   Now, upon closer inspection I do see that bioconductor-deseq2 is listed as a dependency and that dependency was not resolved in the installa…

deseq2 galaxy

updated 8.7 years ago • gkuffel

threshold-based Wald tests by using the lfcThreshold and altHypothesis arguments to the DESeq2::results function. However, I noticed in the DESeq2 (2014 _Genome Biology_) paper, it stated in page 6 "DESeq2 offers...is no way to do threshold-based Wald tests on the shrunken LFC values in recent versions of DESeq2. Is my understanding correct? I did some test ru…

deseq2

updated 8.1 years ago • Lei

option (it is meant to score counts using abundance estimates scaled up to library size) since DESeq2 uses un-normalized data and since by the "counts" function it is possible to get normalized counts

deseq2 tximport normalization salmon rnaseq

updated 7.8 years ago • ginlucks

I am using DiffBind to create a count matrix as summarizedExperiment and then running this through DESeq2 and I was wondering about ways to filter for specific baseMean ranges within this data? My script looks like the following...pre> library("DESeq2") library("ggplot2") library("BiocParallel") library("DiffBind") parallel=TRUE BPPARAM=MulticoreParam(4) # Create a dba.count...se&am…

deseq2 diffbind basemean summarizedexperiment

updated 7.4 years ago • rbronste

Hi, I used DESeq2 to identify genes that vary with age. I am now wondering whether DESeq2 can also be used to predict age from gene expression

Bioconductor

updated 9 weeks ago • picasa1983

Dear all, I am new to RNA seq data analysis. I have been trying to do some DE analysis using DESeq2. I am comparing two conditions, and I expect two genes X and Y to differ in these conditions. When I put condition 1 as reference

deseq2 apeglm

updated 6.4 years ago • Meghdad

Dear all, we run DESeq2 using the standard approach described in the manual, including filtering through the rowsums function, starting...used just to filter out low-expressed genes, than the remaining raw counts would be processed with DESeq2 under the standard approach. Would this be fine for DESeq2? Thank you for helping

DESeq2

updated 3.7 years ago • luca.s

Hallo, I have trying to perform DEseq2 analysis on my data. Some samples are sequenced in single end mode and some are in paired end mode. I would like to include...Hallo, I have trying to perform DEseq2 analysis on my data. Some samples are sequenced in single end mode and some are in paired end mode. I would like to include this in the design when creating DESeq2 object. Here is the example …

deseq2 multiple factor design

updated 7.7 years ago • 1992

the LRT in DEseq2 make the similar format results to wald test, but log2FoldChange has another mean which I can't understand. so I wonder...if the result of DEseq2 by LRT could be used in SPIA or GSEA directly. If not, how to apply it with SPIA or GSEA? could anyone help me? thank you

deseq2

updated 6.4 years ago • qq809825706

I don' have any interest in between group differential expression analysis. I already follow DESeq2 tutorial but I only get the fold change difference for 2 groups, normal and disease. So, the question is, I want to check...difference between 1 and 2, 1 and 3, and so on, until 1 and 14. So, is this method possible to do in DESeq2 and probably you can share your idea how to do this with D…

deseq2

updated 10.6 years ago • bharata1803

normalized by gene length and alignment quality. There's a lot of posts stating that EdgeR and DESeq2 should (usually) only be used on raw counts, but that is in the context of standard transcriptomics workflows, not metagenomics...would it be appropriate to use the humann2 output for differential abundance analysis with EdgeR or DESeq2? What if the data was just normalized by alignment quality…

edger deseq2

updated 8.0 years ago • nyoungb2

Hello, I'm trying to get my head around some DESeq2 results and I would really appreciate some help. I have two conditions (control and disease) and one continuous variable...time points but I'm working with post-mortem tissue so this is the best i can do). I have set my DESeq2 design as `~condition+age+condition:age` From `resultsNames(dds)` I get: [1] "Intercept" "condition_…

deseq2 R rna-seq design

updated 5.0 years ago • raquelgarza95

I'm trying to install Deseq2 in my Linux computer. I have Ubuntu 20.04. But I got the following warning messages: ```r > warnings() Warning messages: 1...geneplotter’ had non-zero exit status 12: In install.packages(...) : installation of package ‘DESeq2’ had non-zero exit status ``` Then, I installed **libxml2-dev** (sudo apt install libxml2-dev) and **libcurl4-openssl-dev** (sudo ap…

DESeq2 R

updated 4.6 years ago • Gimena

I've updated R and RStudio to the latest versions, and the DESeq2 library does not load due to the error below. I've also uninstalled and reinstalled both BiocManager and DESeq2 but...the error persists: ```r > library(DESeq2) Error: package or namespace load failed for ‘DESeq2’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there

DESeq2 error package library

updated 3.1 years ago • Crystal

Enter the body of text here I tried to install DESeq2 multiple times through various means and I am still getting back error messages. I have a project due Saturday that...I need DESeq2 for and would really appreciate any help! Thank you :) library(DESeq2). Error: package or namespace load failed for ‘DESeq2

DESeq2

updated 2.9 years ago • Chatura

Hello! I'm trying to use USeq's Defined Region Differential Seq (DRDS) app, which uses DESeq2. I installed the package directly from Bioconductor, and but when running the script, I get an error that the function...found. I looked up rlog in DESeq and only found rlogTransformation(). I believe that's an error in DESeq2, but I'm kind of new to all this so I'm not sure. Does anyone have any sugg…

DESeq DESeq2 DESeq DESeq2

updated 11.4 years ago • Guest User

I'd like to perform variance stabilization transformation in DESeq2 but got this error message. Any input would be much appreciated. Thank you.   vsd <- vst(dds, blind = TRUE) Error in vst...I'd like to perform variance stabilization transformation in DESeq2 but got this error message. Any input would be much appreciated. Thank you.   vsd <- vst(dds, blind =…

deseq2 variancestabilizingtransformation

updated 8.4 years ago • anpham

I have some questions about rlog transformation using DESeq2: 1) This transformation normalizes for library size, which is sequencing depth or total number of mapped reads, correct

rlog transformation deseq2

updated 9.2 years ago • anpham

if anyone had a pipeline for calculating distances by Bray-Curtis and plotting a PCOA plot with a DESeq2 object? The plotPCA function doesn't seem to give you the option to choose which distance metric to use. If anyone has

deseq2

updated 6.7 years ago • amgodogma

gt; install.packages("DESeq2") Installing package into ‘/home/z800/R/x86\_64-pc-linux-gnu-library/3.2’ (as ‘lib’ is unspecified) Warning in install.packages...nbsp; package ‘DESeq2’ is not available (for R version 3.2.3)   Does it mean I need download R version earlier

deseq2

updated 8.8 years ago • 1151328872

header=TRUE,row.names=1,sep="\\t") \#removing rows that are zero for all genes (edgeR and DESeq have trouble with these) x <- rowSums(rawcountData...this file before starting the analysis colData <- read.table("sample-info.tbl",header=TRUE,row.names=1,sep="\\t") \#Make DESeq2 Object dds <- DESeqDataSetFromMatrix(countData = filteredcountData,colData = colData,desig…

deseq2

updated 10.8 years ago • gokhulkrishnakilaru

I want to use DESeq2 for analyze my miRNA data. In the vignette from DESeq2 I didn't quite understand which input file we should use for Differential...Expression (DE) analysis. I processed my data using miRDeep2, now I need to use DESeq2 to do the DE. Is there any step before DESeq2? Can I go from miRDeep2 results straight to DESeq2

DESeq2

updated 3.2 years ago • Mariane

Hi, I ran diffbind and used edgeR and DESeq2. I have a question regarding the normalized counts. In the DESeq2 analysis, the normalized counts of one of the samples...column with integers. In EdgeR normalization - one column is chosen as reference to all, and in DESeq2 they create another column of the averages that is ussed for normalization. So In EdgeR I would expect to have after.…

diffbind normalized counts

updated 9.5 years ago • GFM

like in the example: DrugvsPlacebo.1h = (Drug.1h-Drug.0h)-(Placebo.1h-Placebo.0h). Reading the DESeq2 manual I can use contrast using a list of two character vectors or a numeric contrast vector. Both requires to use the...using all the experimental factors combined into one combined factor (group column) using DESeq2? Thank you. [1]: https://bioconductor.org/packages/release/bioc/v…

deseq2

updated 5.7 years ago • ribioinfo

Dear DESeq2 developer and colleagues, DESeq2 generates an output table including "log2FoldChange". I have two questions about

deseq2

updated 6.5 years ago • bioinfo

Dear all, I am using DESeq2 to identify differentially expressed genes between two conditions. This is a summary of my code: dds-tvsc <- DESeqDataSetFromMatrix...Dear all, I am using DESeq2 to identify differentially expressed genes between two conditions. This is a summary of my code: dds-tvsc <- DESeqDataSetFromMatrix(countData = cd-treated-vs-control_matrix, c…

deseq2 apeglm

updated 5.4 years ago • josmantorres

Hello,   I have a question about the DESeq2 package. My experiment is comprised of eight different treatments, which I am analyzing in pairs. I did the DESeq2 analysis

deseq2

updated 7.9 years ago • meshi.barsheshet

Hello, I am very new to this and it might be a very easy one line fix, but I have a quick question about running DESeq2 for 3 samples groups. I performed ATACseq and RNAseq on 24 different patient samples across 3 different subtypes of leukemic cells (subtypes "E", "H", and "D".  I want to see what sites/genes are specific to each subtype using DESeq2.  I generated a Matrix wi…

deseq2

updated 7.2 years ago • jonathan.diedrich

Hi,   I have used two different versions of DESeq2 (1.16 and 1.18) and they give me completely different results loosing a lot of differentially expressed genes! Since

deseq2 mikelove

updated 7.9 years ago • marika.catapano

platform) : 1- How can I check if these batches are some effects on my data? 2- Is right to put in DESeq2 formula all batches to perfom DE analysis or I should use other methods?<span style="line-height:1.6">  </span> Thank

deseq2

updated 9.9 years ago • arinaldi

2013 at 10:56 PM, Jon Lees <jonglees@gmail.com> wrote: > Dear Prof. Love > > Im using the deseq2 package, its giving us really nice results. > and seems to fix some issues over deseq2 with our data. > > I just had quick

DESeq DESeq2 DESeq DESeq2

updated 12.7 years ago • Michael Love

As part of that pipeline, I would like to calculate the differentially expressed genes using DESeq2. Initially, I am working with a Seurat Object, as such I run the following code to achieve what I would like to do: exp_mtx...lt;- as.data.frame(matrix(NA,length(colnames(exp_mtx)),1)) names(exp_design) <- c("cluster") row.names(exp_design) <- seurat_exp_mtx@meta.data$ce…

DESeq2 Scrna scRNAseq

updated 4.4 years ago • RDoc

please tell me about DESeq2 codes

DFP

updated 4.5 years ago • Mairembam Stelin

In the past, (DESeq2 versions < 1.1.4), MA plots from DESeq2 looked like the following (formatting modified by me, but you get the idea). <img

deseq2 maplot

updated 8.2 years ago • jshouse

microRNA from 32 samples (16 treatment vs 16 control), and I've got a count matrix. While using DESeq2 to looking for DE, I found the padj for all microRNAs are as high as > 0.99. Following is my code, any help would be appreciated...library(DESeq2) dds <- DESeqDataSetFromMatrix(myframe, coldata, ~ treatment) dds <- DESeq(dds) res <- results(dds) re…

deseq2 RNA-seq microRNA

updated 5.6 years ago • saulwang0102

I am getting drastically different result when analysing a dataset using different version of DESeq2. I'm repeating DE analysis I did last year, with a previous version DESeq2 - specifically, DESeq2 1.4.5, under R3.1 Spring Dance - and I am seeing completely different results with the current version, which is is DESeq2 …

deseq2 differential expression microbiome

updated 10.3 years ago • drei

I am looking to extract the normalized FPKM values that DEseq2 uses for it's models. I know that it it likely is not stored. Is there a way to generate them?&nbsp

deseq2

updated 9.6 years ago • cchow

Hi Michael and community, Thanks for the work and efforts on DESeq2! I've had this question for some time, I went through quite a number of posts, the manual, and the vignette, but can't really...TRUE", and  "transform = TRUE" arguments. So is the y axis just raw read counts divided by DESeq2-estimated size factor? or has it been logged? (loge? log2? log10?) Also, why is the psudocount …

deseq2

updated 7.9 years ago • Alan

days (D0 and D3), different cell groups (high and low) and two conditions (WT, KO). All are in duplications (see table below) names day condition differentiated rep 1 D0_MAEAKO_High_1 D0 KO high 1 2 D0_MAEAKO_High_2

deseq2 design metadata

updated 6.0 years ago • Assa Yeroslaviz

Hi, I tried to install DESeq2 in an renv managed environment. I kept getting the following error: > BiocManager::install("DESeq2") Bioconductor version...Installing package(s) 'DESeq2' …

deseq2

updated 5.6 years ago • christoph.kaempf

nbsp;Hello all, I am experiencing strange results from the output of DESeq2. I am getting many genes that have low counts in the conditions I am comparing. This is one striking example where a gene...is.na(resOrdered$padj),] resOrderedSDE <- resOrdered[resOrdered$padj < 0.05,] any(row.names(resOrderedSDE) == "Xelaev18000166m|Xelaev18000166m") [1] TRUE plotCounts(dds18, "X…

deseq2

updated 7.9 years ago • rrcutler

Dear Community,   I am new to do differential gene expression analysis uisng DESeq2. I have a set of 380 genes sequenced and i ran DESeq2 to find genes significantly expressed. However i read that DESeq2...Dear Community,   I am new to do differential gene expression analysis uisng DESeq2. I have a set of 380 genes sequenced and i ran DESeq2 to find genes significantly expre…

deseq2

updated 7.7 years ago • suranandbabu85

the original data set. Please help.  2. How can i verify that the subset of genes selected by deseq2 is the best subset

deseq2

updated 7.8 years ago • me37uday

all, I do DGE analysis (sample A vs sample B) using Salmon then Tximport (without scaling) then DEseq2. Everything works fine but my problem is that sample A is contaminated with red blood cells so that half of the total...less than 10 transcripts, easy to identify) from the TXI output file before loading into DESeq2? If doing so, should I use scaledTPM values? Thank you for your help. Bruno …

deseq2 salmon tximport

updated 8.4 years ago • bruno.saubamea

Hi there, Just got a couple of questions for DESeq2: 1. To build a design including paired samples (i.e. Subject) and batch variables (as estimated by SVA, i.e. SV1 and SV2), and...the same lfcThreshold? therefore to enable a more direct comparison between RNA-seq (DGE using DESeq2) and microarray (DGE using limma) data for the same samples. Thanks Guan

deseq2

updated 6.2 years ago • guanwang179

I am trying to use deseq2 to compare differential gene expression across multiple generations of repeated treatment. I have three replicates...control vs treated - 3 time treatment: control vs treated So far, I have been running deseq2 on each generation separately since each generation has their own control. However, I want to be able to compare between...generations and was wondering if i…

rnaseq deseq2

updated 2.7 years ago • lunarskye222

Hi, I'm quite sure I have a problem with the DESeq2 independent filtering. DESeq2 doesn't flag any outliers when performing the DE analysis. We have little concern about...Hi, I'm quite sure I have a problem with the DESeq2 independent filtering. DESeq2 doesn't flag any outliers when performing the DE analysis. We have little concern about blood being in the samples as the raw counts vary from …

deseq2 filtering outliers count outliers

updated 8.4 years ago • heikki.sarin

Hi Michael and community, As always, thank you for your devotion in DESeq2. I'd like to ask about: is it reasonable to to run DESeq2 analysis on only a "subset" of the original raw count matrix? (would...Hi Michael and community, As always, thank you for your devotion in DESeq2. I'd like to ask about: is it reasonable to to run DESeq2 analysis on only a "subset" of the origina…

deseq2

updated 7.9 years ago • Alan

Hi, I am trying to understand and compare the DESeq2 model and the BNB-R (https://github.com/siamakz/BNBR) model. The corresponding references are: - DESeq2: Love, M. I., Huber, W., &amp...Anders, S. (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology, 15(12), 550. https://doi.org/10.1186/s13059-014-0550-8 - BNB-R: Dadaneh, S. …

DESeq2 BNB-R

updated 6.9 years ago • Homer

Hello.. I am having trouble properly installing DESeq2. Currently have R version 4.0.2, trying to install with Bioconductor version 3.11. I tried troubleshooting with some...I have tried commands for installing the package survival individually. The command library('DESeq2') results in an error message: Error in library("DESeq2"): there is no package called ‘DESeq2’. I would appreciate any help w…

deseq2 survival

updated 5.5 years ago • hall.brooke33

RNAseq data. I recently updated my R version via an uninstall/re-install and now can no longer get DESeq2 to install or run properly. When trying to install with <pre> > source("https://bioconductor.org/biocLite.R") > biocLite...DESeq2")</pre> I get the following errors:  <span style="background-color:Yellow">BioC\_mirror: https://bioconductor.org …

bioconductor r deseq2

updated 8.8 years ago • tscharschmidt

It's recommended to do RUV correction before DESeq2. However, the PCA doesn't show any clear separation between the groups. How can I know if my data needs further pre-processing...before DESeq2? Is there any metrics or plots that can guide me? ![enter image description here][1] [1]: /media/images/30ab2b39-6893-4c5e-9531

DESeq2 PrincipalComponent prin DifferentialExpression

updated 23 months ago • Shaimaa Gamal

Hello Mike, I have one question about the DESeq2 model. Given that I have 2 groups of RNA-seq, each of which has 3 biological replicates. Thus, each gene has 3 biological...replicates in each condiction. does the DESeq2 model use average gene expression or each replicate of gene to estimate paratmeters, such as beta and intercept? Thanks

DESeq2

updated 2.8 years ago • BioEpi

in one big matrix, I lose the difference in intensity between these genotypes presumably because DESeq2 calculates across the entire matrix. Instead, the normalized counts for both genotypes come up close to equal. In reality...of experiments and should not have equal normalized counts. If I normalize WT and KO separately with DESeq2 (two separate DESeq2 objects for either WT or KO), the ratio is…

deseq2

updated 9.2 years ago • snamjoshi87

any plans for transcript level differential expression (I.e. Supporting fractional counts), with DESeq2?? &nbsp

deseq2

updated 10.6 years ago • andrew.j.skelton73

span style="line-height:1.6">While running DESeq2 on a Human dataset (commands given below), I have noticed the following error. How I can handle my data with this case...p/63845/>? Could you tell me how to solve the problem, please? > library("DESeq2") > setwd("/folder/to/path/") > sampleFiles =grep("count",list.files("/folder/to/path/"),value=TRUE) …

deseq2

updated 10.9 years ago • ygchai2015

to correct for this variance. This is why I’d like to skip the estimateDespersions() function in DESeq2 and continue with the nbionamWald() function directly after library normalization. However, this function requires...w64-mingw32/x64 (64-bit)</pre> <pre> Running under: Windows 7 x64 (build 7601) Service Pack 1</pre> ‘DESeq2’ version 1.10.1

deseq2 estimatedispersions

updated 8.6 years ago • nicky.driedonks

Dear all I am a working with DESeq2 (version 1.22.2) on R (version 3.5.3) to analyze my data from RNA sequencing. I did some tests last week and I had no trouble...1] "Intercept" "condition1" "taille" ``` Why don't I have the same name as last week? Is my DESeq2 analysis good ? I tried to find the answer but I do not know where is the problem. Thank you for your help ! Emilie

deseq2

updated 6.1 years ago • emilie.derisoud