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

I am using below design for DESeq2 analysis, how I can change below PCA CODE to make PCA based on Treatment and compartment? dds$group <- as.factor(paste...local') PCA<-plotPCA(rlddds, intgroup = "Treatment", returnData = TRUE) write.table(PCA, "DESeq2-pca-table-rld", row.names=TRUE, sep="\t"); pdf("DESeq2-pca-5Family-table-rld.pdf"); plotPCA(rld5Family, i…

deseq2

updated 5.6 years ago • nabiyogesh

The question is: We will run the analysis with two factors but without an interaction term. You need to be careful in how you specify the design, as results() will by default return...specify the contrast you want to perform. my code: <pre> res<-results(dds) dds$condition <- factor(dds$condition, levels = c("untreated","treated")) UvsT<-results(dds, contrast=c('co…

deseq2

updated 8.1 years ago • hira_sehu

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

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

Hello Everyone, I am using DESeq2 for DEG analysis. I have a total of 8 samples( 1 duplicate for each condition so 4 different conditions) At this point...Hello Everyone, I am using DESeq2 for DEG analysis. I have a total of 8 samples( 1 duplicate for each condition so 4 different conditions) At this point of

deseq2

updated 6.7 years ago • Merlin

Hi, when I got my DESeq2 analysis result, I found the log2Foldchange values are between -1 to 1. But when I checked the normalized read counts...lt;- merge(normCounts, significant, by = 0) write.csv(allsig, "allsig.csv") ``` and below are the first few lines of file allsig.csv after sorting by log2Foldchange values: ```r Row.names tissue1-1 tissue1-2 tissue1-3 tissue2

DESeq2

updated 4.1 years ago • Cheryl

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

and am trying to come up with a model design to compare the differences between 2 treatments and 2 factors. I need help in trying to organize the model design matrix in EdgeR. How can I write the code for them to be recognized...1" cellspacing="1" style="width:500px"> <thead> <tr> <th scope="row"> </th> <th scope="col">Factor #1</th> <th scope="c…

edger design model interaction model rnaseq

updated 7.0 years ago • cody0071

influence ,  2samples for mant, 3 for late\_treated, 1 for mesenchymal\_stem\_cells) The size factors are very different (look HMSC\_tot and T6rep2).  <pre> "SIZEFACTORS: " mantrep1 mantrep2 t6rep1 t6rep2 t6_2015 HMSC_tot...something must goes wrong here !! Can we compare samples with very different library size ? However DESeq2 model internally corrects fo…

deseq2

updated 9.2 years ago • ZheFrench

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

Hey everyone, this is my first question in the forum.  i'm analyzing RNA-Seq data of Tomato.  some of the samples were treated with HeatShock...Hey everyone, this is my first question in the forum.  i'm analyzing RNA-Seq data of Tomato.  some of the samples were treated with HeatShock, and...my question how does it effects other genes at the phase of norm…

deseq2 rnaseq tomato geneexpression

updated 9.8 years ago • hamaor

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

all cell lines as well as the DBs that are unique to each cell line. I have tried the blocking factor in diffbind, and got two lists of DBs from analysis with and without blocking factor. Is there built-in functions in Diffbind

diffbind differential binding analysis blocking

updated 7.9 years ago • zhangly811

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

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've recently done some DE analysis with DESeq2, with relatively small sample sizes. The experimental setup is a time course of 4 points, with matched samples of two...0, 0, 0, 0, 1, 0, 0, 0, 1)</code> Looking for the genes with maximal fold changes in the size factor-normalized counts identifies a large number of very similar genes (i.e. names identical apart from a number, no dif…

deseq2 rnaseq differential gene expression

updated 9.8 years ago • willmacnair

Hi I am new user of DESeq2 and have few questions regarding the design formula, results, and their inferences: I am having four cell types (A,B,C...Hi I am new user of DESeq2 and have few questions regarding the design formula, results, and their inferences: I am having four cell types (A,B,C,D...countData = count2,colData = traitdata2,design = ~Age + CellType) dds2$group <- factor(…

deseq2

updated 9.3 years ago • rammohanshukla

Dear all, I have a question regarding DESeq2 package. Please help. I am using this package to analyze a RNA seq dataset. The dataset has  3 different groups and...dat0,colData=pheno,design=~ State) #condition #relevel groups dds.fc@colData$State<-factor(dds.fc@colData$State,levels=c("non-infected spleen","infected lung","infected spleen")) dds<-DESeq(dds.fc,test = "LRT"…

deseq2

updated 9.4 years ago • szenitha

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

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 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

post H01 Placebo M ``` I know that Sample_Group is my within-individual factor and Treatment is between-individual factor, but still do not get answers. Here is my code. I would really appreciate if...anyone can help me. I am so confused. ``` groups <- factor($targets$Sample_Group) ## pre & post treatment <- factor(targets$Treatment) ## Rapamycin &am…

limma technical replicate

updated 6.3 years ago • sh.kazempour94

Hello, I am looking for some guidance in how to best set up/carry my hypothesis testing in a situation where I have a phage infecting a bacterium. We have three genotypes, four time points for infected samples, and two time points for uninfected samples. I have a count matrix that was generated using featureCounts after alignment of reads using bowtie2, and the matrix includes reads mapping…

RNASeq DESeq2

updated 2.2 years ago • Sean

Hello, I would like to use DESeq2 on ATAC-seq data from human disease and control individuals. I know based on PCA plot that age is a big confounder. So...Hello, I would like to use DESeq2 on ATAC-seq data from human disease and control individuals. I know based on PCA plot that age is a big confounder. So, I...want to first correct for age as a covariate, and *then* use RUVseq on the age-cor…

DESeq2 RUVSeq

updated 3.1 years ago • Lisa

Hi, I am in the process of analyzing RNA seq data for an experiment in ants with three factors. Factor 1: presence/absence of queens (levels:present, absent) Factor 2: sample type (levels: forager, nurse, larva, etc.) Factor...mostly following section 3.3.3 and 3.3.4.  We want to be able to analyze the effect of all factors, as well as pairwise interactions. For questions using all …

edger nested design rnaseq

updated 10.6 years ago • mrwarner09

<div class="preformatted">Dear Roman, I know that your question was specifically about the DESeq package, but you have previously asked about the edgeR, bayseq and DESeq packages on SEQanswers: http://seqanswers.com/forums/showthread.php?t=4349 so I thought you might appreciate a more complete answer. I think that edgeR is the only package on Bioconductor that analyses RNA-Seq experim…

RNASeq edgeR baySeq DESeq RNASeq edgeR baySeq DESeq

updated 14.7 years ago • Gordon Smyth

of the others and must be removed. I followed the instructions reported in the vignette of DESeq2 in case of Group-specific condition effect, which is the case of my experimental design, but I am not able to solve the...script: counts <- data.frame(final_counts_clean) samples <- data.frame(condition=factor(rep(c("HN","LN"),each=6)), phenotype=factor(rep(c("HLR", "…

DESeq2

updated 4.5 years ago • claudia

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

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

Hello, Im currently re performing some analyses of RNA-seq data via DESeq2, however since the first analysis (about a year ago) Ive got some very strange genes turning up as significantly expressed

deseq2 rnaseq

updated 7.0 years ago • taamslab

am confused as to where should I write the contrasts? Can you please explain the difference between factor levels and contrasts? Thank you for your help. ```r # load libraries library(DESeq2) # Step 1: preparing the count data # read in...se, design = design, ignoreRank): some variables in ## design formula are characters, converting to factors ## Note: levels of factors in the design con…

DESeq2

updated 3.8 years ago • Manav

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

length(row[row>5]) > 2),] ``` I then import this count matrix and proceed as normal using DESeq2 (that is using the default normalization) ```r DDS <- estimateSizeFactors(DDS) DDS <- DESeq(DDS, test = "Wald") ``` Running a Wald...test in DESeq2 on this yields results almost identical to those I get with csaw and diffbind, the general trend in sites is the same..…

csaw ChIPseq DESeq2 DiffBind

updated 9 months ago • Luca

Hello, we're working on a differential expression (DEG) analysis using DESeq2 for a dataset involving an eukaryotic host experimentally infected with a virus. Dataset: Our design includes comparisons...to a key question: Should we perform DEG analysis on the combined host + virus transcriptome in DESeq2, or analyze host and viral genes separately? A different post [here][1] suggest…

DESeq2

updated 7 months ago • Bárbara

style="line-height:1.6">Transcription factor expression </strong><span style="line-height:1.6">(continuous).</span>   We are interested in    1. What is the age...A and Strain B in age\*genotype effects.  4. Does the expression level of the transcription factor have an effect on RNA expression.    For the first 3 qu…

limma limma design matrix multiple factor design

updated 9.8 years ago • ashley.lu01

ind.n values since I did 3 experiments. I used the following "metadata_ls_age_2" for deseq2 analysis, subsetted for the specific timepoint I'm having trouble with. (in addition to a matched count matrix called...of running the following in an R session sessionInfo( ) ``` Here is the script I used to run deseq2 ``` i <- "120" idx <- which(names(counts_ls_age) == i)…

DESeq2

updated 2.0 years ago • JalapenoCornbread

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

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

AffyBatch...done. Computing expression calls... ..........done. scaling to a TGT of 100 ...Scale factor for: 1.CEL 1.27818905696529e-247 Scale factor for: 2.CEL 8.30729457715284e-252 Scale factor for: 3.CEL 1.27818905696529e...247 Scale factor for: 4.CEL 1.27818905696529e-247 Scale factor for: 5.CEL 2.37641150479280e-156 Scale factor for: 6.CEL 2.37641150479280e...156 Scale factor for: 7.CEL 1.27…

probe simpleaffy probe simpleaffy

updated 20.8 years ago • Georg Otto

heatmap. So fare, I am using the DiffBind R package and I would like to show the correlation factors in the heatmap as numbers in the different tiles or as an alternative save the matrix, which is used to generate the...heatmap to take the correlations factors from there. I am using ChIP-Seq data to investigate different Binding behaviours of a Hox transcription factor, for...to the heatmap but…

DiffBind

updated 4.1 years ago • Katrin