Bioconductor Forum

Dear all, I am new to RNA-seq analysis with bioconductor. I am wondering if I can use DESeq2 directly to perform survival analysis (e.g. Cox regression)? If not directly, do I understand correctly that we should

deseq2 survival rlog transformation

updated 8.3 years ago • array chip

Hi, I want to use deseq2 for RNAseq analysis. I have excel file of RNA count data with one column is geneid and others are different patients

deseq2

updated 5.4 years ago • shinemuty

I used DESeq2 and found it report more deferentially expressed genes than before. Actually, it is not reasonable. I noticed the `` padj...pvalue column). I would like you to tell me the incorrect of my calculation, or some bugs in DESeq2. Thanks a lot. In the following, I pasted my sessionInfo()   <pre> > sessionInfo() R version 3.1.0 (2014-04-10) Platform: x86_64

Bugs deseq2

updated 11.4 years ago • lmf.bill@gmail.com

Hi, I'm trying to understand the normalization for DESeq2 analysis within DiffBind.  If I run: <code>Pool1 = dba.analyze(Pool1,method=DBA_DESEQ2,<strong>bFullLibrarySize...Hi, I'm trying to understand the normalization for DESeq2 analysis within DiffBind.  If I run: <code>Pool1 = dba.analyze(Pool1,method=DBA_DESEQ2,<strong>bFullLibrarySize=FALSE</s…

diffbind deseq2

updated 10.8 years ago • JasonLouisStein

Dear all, I have been using DESeq2 for RNA sequencing-based gene expression analysis, and recently trying to use ARACNe for regulatory network inference

deseq2

updated 6.5 years ago • Tom

is any hidden structure in this cell population. I was thinking of performing PCA. I wanted to use DESeq2 but their workflow seems to involve computing the differential expression first: <pre> ddsHTSeq<-DESeqDataSetFromHTSeqCount...or depend on computing differential expression between 2 or more groups. How can I do this? If DESeq2 can't do this can you recommend an alternative? &…

rnaseq pca deseq2 clustering

updated 10.8 years ago • Nick N

I conducted differential expression analysis using limma over several datasets separatly. Now I have several dataframes containing the differential expression analysis for those datasets, and I want to show them on a volcano plot using the MetaVolcanoR package. If it matters, each dataframe contains a different number of genes. All of them together have about 1900 genes, with 322 duplicate genes…

limma MetaVolcanoR EnhancedVolcano

updated 3.6 years ago • JAcky

lt;- results(B_ddsTxi, c("condition", "Y", "X")) B_res$symbol <- mapIds(Mus.musculus, keys=row.names(B_res), column="SYMBOL", keytype="GENEID", multiVals="first") B_res$chrom <- mapIds(TxDb.Mmusculus.UCSC.mm10.knownGene...keys=row.names(B_res), column="TXCHROM", keytype="GENEID", multiVals="first") B_res$strand <- mapIds(TxDb.Mmusculus.UCSC.mm10.knownGene...keys=row.name…

AnnotationDbi annotation TxDb.Mmusculus.UCSC.mm10.knownGene

updated 5.7 years ago • 94133

Hi all, Salmon produces transcript counts and some include decimals. I noticed that if I import my quant files from salmon (244 files) with non-integer values and then run DESeq I detected 327 DE genes. txi <- tximport(files, type = "salmon", tx2gene = txdf, ignoreTxVersion = T) ddsTxi <- DESeqDataSetFromTximport(txi, colData = samples, design = ~ RSV_NPA) ddsTx…

deseq2

updated 5.7 years ago • mlosada323

Hi, I’m performing a DEG analysis with RNA-seq data using `salmon` + `DESeq2`. The data were obtained from different parts of cerebral tissue and I am expecting to get a few differentially expressed...in my contrasts, because our case/control samples are quite similar (in a PCA). As described in `DESeq2` vignette, I’ve summarized transcripts estimated counts into gene counts, following `tximport`…

deseq2 edgeR salmon tximport

updated 5.8 years ago • iaradsouza1

diagnostic test for outliers called Cook’s distance caused DESeq2 (version 1.10 vs 1.30) have big different result? anyone find similar issue

version1.30 version1.10 deseq2 DESeq2

updated 4.4 years ago • Shicheng

designs with interactions_. Is there a way to get shrinked LFC values for designs with interactions? DESeq2\_1.19.14 Thanks, YK

deseq2 lfcshrink

updated 8.1 years ago • yk.gatc

Hi there, I noticed that the lfcshrink() function in DESeq2 doesn't seem to work with more complex contrast designs, eg: those with interaction terms. Is it possible for this to...Hi there, I noticed that the lfcshrink() function in DESeq2 doesn't seem to work with more complex contrast designs, eg: those with interaction terms. Is it possible for this to be

deseq2 lfcshrink interaction term

updated 7.8 years ago • krutherford

The final step of DESeq2 dispersion estimation takes a very long time to run on a dataset with 27 groups . I was wondering if there is a good strategy

rnaseq deseq2

updated 10.2 years ago • mchikina

reproducibility argument hold (between two experiments) or should one disable log2FC shrinkage in DESeq2? Thanks in advance.   &nbsp

deseq2

updated 8.8 years ago • m.f.g

preformatted">Dear Michael Love and list members, I'm used to analyze RNA-seq data with your nice DESeq2 package (1.2.0) and I sometimes have to test complex null hypotheses using contrasts. For one of my project, I would like...in results(), but it only accepts a numeric vector. Hence, I was wondering if you planned to extend DESeq2 to the use of multiple contrasts? Best regards, Hugo --…

DESeq2 DESeq2

updated 12.2 years ago • Hugo Varet

Hi Bioconductor community! I'm using DESeq2 to visualize which taxa are significantly enriched in one treatment over a control and realized that [the vignette...Hi Bioconductor community! I'm using DESeq2 to visualize which taxa are significantly enriched in one treatment over a control and realized that [the vignette](http://joey711.github.io/phyloseq-extensions/DESeq2.html) doesn't result in …

deseq2 metagenomics phyloseq ggplot2

updated 8.5 years ago • lauren.czaplicki

genes for RUVg were obtained using a cutoff of pvalue > 0.5 and design = ~ litter + condition in DESeq2. My question is whether I should still account for the 'litter' factor in my DESeq2 design after taking into account the

deseq2 normalization

updated 7.1 years ago • jonathan.limwc

Hi All, I have received read counts per gene (48K genes) per sample after RNASeq data processing. Now I need to create heatmaps for these samples. Here is what I did: I had two types of stem cells (iPSC and ES cell) which were differentiated to three lineages in parallel (iPSC-0, iPSC-1, iPSC-2; ES-0, ES-1 and ES-2). I have 2 questions: 1. I want to analyze the read counts by DESeq2 but to my k…

deseq2 normalization

updated 5.8 years ago • Hamidreza Hashemi

I was wondering how one can do a deseq2 analysis of multiple time points when trying to test for a WT vs TREAT difference at any of the given times. Let's say...I was wondering how one can do a deseq2 analysis of multiple time points when trying to test for a WT vs TREAT difference at any of the given times. Let's say I...or to compare changes in all TP. I'm interested to understand how th…

deseq2 time-series design matrix edger

updated 7.0 years ago • Assa Yeroslaviz

Hello everyone! My question is related to RNA-seq analysis utilizing DESeq2. Input: I try to analyze DEGs between normal HEK293 cells and HEK293 depleted by one protein. So, I have 3 biological replicates...Hello everyone! My question is related to RNA-seq analysis utilizing DESeq2. Input: I try to analyze DEGs between normal HEK293 cells and HEK293 depleted by one protein. So, I ha…

deseq2

updated 6.0 years ago • alexandr.gopanenko

Hi there, I've run DESeq2 on an RNA-seq data sets, with the count data came from HTSeq count. The DESeq() call was all by default. &nbsp...why were they not filtered out by the cook's distance or independent filtering? versions:  DESeq2\_1.18.1, R\_3.4.2. Any explanation will be greatly appreciated

rnaseq deseq2

updated 8.2 years ago • wbliu

I'm trying to use DESeq2 to perform something like a one-way ANOVA on 3 groups of samples. I've seen the same question and answer here: https://support.bioconductor.org...I'm trying to use DESeq2 to perform something like a one-way ANOVA on 3 groups of samples. I've seen the same question and answer here: https://support.bioconductor.org/p/61563/ However, I can't seem to  g…

deseq2

updated 10.4 years ago • jenniewoo

Hello, I am running DESeq2\_1.10.1 on a data set with a continuous predictor term (either with or without a categorical blocking term).   My...Hello, I am running DESeq2\_1.10.1 on a data set with a continuous predictor term (either with or without a categorical blocking term).   My understanding...inspection of Cook's distances.  I base this on section 3.6 of the N…

deseq2 outliers RNAseq differential gene expression

updated 9.0 years ago • cajawe

Hello, I am new to DESeq2. The vignette ([LINK](http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html)) focuses on a...that in edgeR we could define such a list via: __my.contrasts <- makeContrasts(). __ In DESeq2, according to the vignette and these topics ([Link 1](https://support.bioconductor.org/p/67600/) and [Link 2](https...Th…

deseq2

updated 7.3 years ago • David ROUX

Hello, I am using DESeq2 in phyloseq to analyse my data, following the phyloseq tutorial. Previously I used the following code and this seemed...are quite different. The difference is at the point when I try to convert the phyloseq format to DESeq2 I get the error message in bold below (previously I was not seeing this error message). I have also loaded the sessionInfo

deseq2 phyloseq

updated 9.0 years ago • sarahmacdonald86

is - should the problematic samples be excluded only or the entire subject data to be removed in DESeq2 analysis? Thanks. Regards Guan

deseq2

updated 7.1 years ago • g.wang2

Hi there, I would like to ask about organising my data for DESeq2 - to do RNAseq analysis. How do I not include my first column (gene ID) for my rawcount data as I am unable to cross check my

deseq2

updated 5.8 years ago • angkoo

Hello, Can someone help me to understand the dispersion calculation of DESeq2? I don't understand what does DESeq2 : 1) If we consider two conditions A and B with n samples in each conditions, are the informations...blue on the dispersion plot but it dispersion wil be shrunked by MAP procedure). 2) Or does DESeq2 calculates the mean normalized counts for cond. A (µA) and cond. B …

DESeq2 dispersion

updated 7.1 years ago • eva-m.petit

DESeq2 I installed from latest Bionconductor version is still 1.20 version. Actually, the latest version of DESeq2 is >1.4...Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.5.0   (2018-04-23).   > packageVersion("DESeq2") \[1\] ‘1.20.0’   > sessionInfo() R version 3.5.0 (2018-04-23) Platform: x86\_64-apple-darwin15.6.0 (64-bit) Running under: …

deseq2 R bioconductor

updated 7.6 years ago • lxl623

Hi,  Does anyone have experience with standard rna-seq analysis tools (edgeR, DESeq2, etc) to detect allele-specific expression? I have a count table in which each F1 hybrid (3 biological replicates) has...Hi,  Does anyone have experience with standard rna-seq analysis tools (edgeR, DESeq2, etc) to detect allele-specific expression? I have a count table in which each F1 hybrid…

edgeR deseq2 ase allele

updated 10.4 years ago • trianglescout

Hi, due to a strange error in DESeq my group is finally being forced to switch to DESeq2 (probably a good thing). There is one problem we are not sure how to solve, though: In the old DESeq, we would normalise the...nor with nbinomWaldTest(). Is it in this case recommended to reduce the data set before using DESeq2, for each comparison, or should we try to run the DESeq() function once and the…

deseq2 deseq

updated 8.7 years ago • LilithElina

everyone, just a quick question I am about to generate my volcano plots for DEG analysis after DESeq2. I am wondering if I should use my normal DESeq2 results, or the results I have applied LFC Shrinkage too? What is the reasoning

DESeq2

updated 3.9 years ago • axe880

data sets with triplicates. I was analyzing both the differences in each pair of time-points using DESeq2 as well as the time-series analysis using Mfuzz. I have tried to compare the expression values (or more precise profiles...created by Mfuzz and DESeq2 and got confusing results. Below is an example for one gene, its raw values as well as the calculated values from Mfuzz...and normalised valu…

deseq2 mfuzz differential expression timecourse

updated 9.4 years ago • Assa Yeroslaviz

I am having difficulty installing DESeq2 to my mac laptop. This is what it shows on my screen. When I type in library(DESeq2), it also gives me this warning. Please help...1: package(s) not installed when version(s) same as current; use `force = TRUE` to re-install: 'DESeq2' 2: In install.packages(update[instlib == l, "Package"], l, repos = repos, : installation of package ‘tibble’…

DESeq2

updated 3.8 years ago • Jae Woong

Hi, The following is my deseq2 design and my commands <pre> dds <- DESeqDataSetFromHTSeqCount(sampleTable = sampleTable,directory = directory,design...Hi, The following is my deseq2 design and my commands <pre> dds <- DESeqDataSetFromHTSeqCount(sampleTable = sampleTable,directory = directory,design= ~Sex+V11+V12+V13+V14+V15+V16+V17+Visit,ignoreRank=FALSE) dds &…

deseq2 differential expression results

updated 8.4 years ago • yoursbassanio

Dear experts! The design formula of DESeq2 has been extensively discussed, however, I could not translate any example/explanation to my specific situation...Dear experts! The design formula of DESeq2 has been extensively discussed, however, I could not translate any example/explanation to my specific situation. I have two different transcriptomic experiments and I want to DESeq2 them to…

deseq2

updated 5.4 years ago • Sedlin

Hi, I'm analysing RNA-seq data and I switched from edgeR to DESeq2 because most of my differentially expressed genes had an outlier sample, which was not an outlier in the entire dataset...judged by PCA and overall Cook's distance). My question is related to the criteria used by DESeq2 to count the number of replicates in my experiment. I have 3 experimental groups, A,B and C, each of them wit…

deseq2 ruvseq cookscutoff covariates batch

updated 9.3 years ago • j.viana

expression of the original protein for 6h, about 2000 genes are regulated according to Deseq (not DeSeq2) within Galaxy. I compared triplicates of cells, where the protein was not induced against triplicates of cells, where...i did my experiment the very same way with the truncated protein, there was the new version of DeSeq, DeSeq2. When i run the programm, the output told me, that only 4 gen…

deseq2 truncated protein

updated 10.7 years ago • ChIP-Tease

Hello, I'm hoping to get confirmation that my line of reasoning is correct.  I'm using DESeq2 to test for log2 fold differences in microbial gene abundances across two habitats sampled using metagenomics...Hello, I'm hoping to get confirmation that my line of reasoning is correct.  I'm using DESeq2 to test for log2 fold differences in microbial gene abundances across two hab…

deseq2 normalization metagenomics

updated 10.4 years ago • jessawbryant

I am experiencing problems with adding covariates to my paired samples design in DESeq2. We have 39 paired samples of human subjects (39 untreated samples; 39 treated samples). So in summary, it is a ‘time series...in the effects of treatment on gene expression. Based on the information available in the DESeq2 vignette, I created the following design: <pre> ~ patientID + treatment</pr…

deseq2 deseq paired samples covariates multiple time points

updated 8.4 years ago • imb

within 3 day R Vs S due Treated Vs Control within 7 day My code is > library(DESeq2) countdata <- read.table("Suscep_Resis_ctrl_trt_all_matrix.txt", header=TRUE, row.names=1) countdata countdata...as.matrix(countdata) countdata colData<- read.table ("Metadata.txt", header=TRUE, row.names=1) colData dds…

Deseq2 LRT Factors RNAseq

updated 5.5 years ago • aishu.jp

new("SummarizedExperiment", assays = Assays(SimpleList(counts = m)), colData = DataFrame(row.names = colnames(m)), rowData = DataFrame(row.names = row.names(m)))</pre> <pre> <span style="font-family:sans-serif,arial,verdana,trebuchet...the new object. (This is just an example, I am aware that similar classes already exist, e.g. in the DESeq2 package.)</span> …

summarizedexperiment SummarizedExperiment

updated 9.7 years ago • Thomas Sandmann

replicates from paired normal/tumour samples, different tumours, etc. We've had success using DESeq2 and SAMSeq on raw count data, and the high sample number has been giving low FDRs/q values. We're only interested in a small...I was wondering, then, what are the statistical pitfalls of excluding other genes _before_ input to DESeq2, SAMSeq etc? I'm aware that these apply normalisation whic…

deseq2 SAMseq differential expression

updated 10.0 years ago • aylj

Hi! Quick question about the type of count data DESeq2 expects as input: Should I avoid doing any clean-up prior to normalizing my data with DESeq2?  Currently, I remove...Hi! Quick question about the type of count data DESeq2 expects as input: Should I avoid doing any clean-up prior to normalizing my data with DESeq2?  Currently, I remove contaminant OTUs (those that were pre…

deseq2

updated 10.5 years ago • aravenscraft

I have problems installing DESeq2 using R4.0.4. It tells me that it is not available for my version of R. Does anyone have an idea how to fix this? ```r > BiocManager...install("DESeq2") Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.4 (2021-02-15) Installing package(s) 'DESeq2' trying URL 'https://bioconductor.org...Content type 'application/zip' length 2863628 bytes …

DESeq2

updated 5.0 years ago • reneclassens92

genes on the X and Y chromosomes from my human RNA-seq data before doing differential analysis using DESeq2. I've looked through the _RNA-seq Workflow_ and _DESeq2_ manuals but didn't see this as an option. Any help in performing...this step and still using the DESeq2 or RNA-seq Workflow pipeline would be much appreciated. Thanks

deseq2 rnaseq

updated 7.7 years ago • anpham

I am looking for advice about how to correctly use the "coef" argument to lfcshrink when I am using DESeq2 with a grouping variable. I am analyzing an RNAseq dataset with multiple factors and variables using DESeq2: * SurgeryGroup

deseq2 lfcshrink

updated 7.5 years ago • kendralec

vs baseline, and then comparing each of these subsets to each other using GSEA? Or should I deseq2 using the LRT within each infection (so infection 1 -- 0, 12, 24, 48hrs

deseq2 timepoints

updated 4.8 years ago • ayy2110

nbsp; Dear Mike: I am using DESeq2 to analyse RNA-seq data and very appreciated its comprehensive functionality. In my data, the counts are affected

deseq2

updated 9.3 years ago • zkwu2011

I am trying to understand exactly what DESeq2's `` resultsNames `` outputs. The documentation says: <pre> resultsNames returns the names of the estimated effects

deseq deseq2

updated 11.1 years ago • igor

slightly different than the usual, but I would like to take advantage of the optimal design of DESeq2, so I wonder whether it would be possible to apply it (and how). I have a counts table with columns as different conditions...after correcting by the previous distribution in the pool. Would that be possible to do with DESeq2? I could do it manually but then I wouldn't know how to apply valuable …

deseq2

updated 6.4 years ago • yermatudela

I was trying to plot PCA using DESeq2 `plotPCA` function and `prcomp` function. However, the variances I obtained was quite different. Why is this? ![prcomp PCA...1] ![DESeq2 PCA][2] **Code for PCA using prcomp:** pca <- prcomp(t(countsPC_batch)) percentage <- round(((pca$sdev^2) / (sum(pca$sdev^2))) * 100, 2) pca_data

deseq2 pca hclust

updated 6.4 years ago • ag1805x

Now I wanted to apply the package functionalities to my RNA-Seq data that I already analyzed using DESeq2.  I think the main problem is: how to came up with a  <pre> ExpressionSet data object </pre> from a DESeq2 data object

GOexpress deseq2 expressionset

updated 10.4 years ago • martin.hoelzer

Hello all,   I am analyzing an RNAseq with 6 conditions using deseq2. I have 6 biological replicates for control, however for the other 5 conditions (say C1,C2,C3,C4,C5) I have no replicates

deseq2 differential gene expression

updated 10.4 years ago • ea1402

vs controls) as well as a continuous trait.  While I know that the former can be implemented in DESeq2, I’m not sure whether the latter can; can you comment on this?  If continuous traits can be analyzed, can you provide

deseq2

updated 10.5 years ago • marcus.pezzolesi

I installed Ubuntu 20.04 and R 4.0.1 and I can't install `DESeq2` package. I installed BiocManger using: ``` if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager...BiocManager::install(version = "3.11") ``` When I tried to install `DESeq2` in `Rstudio`, almost all dependencies failed to be installed. So, I opened `R` in the terminal using ` sudo R` comma…

deseq2 install r4.0 bioconductor3.11 ubuntu20.04

updated 5.7 years ago • ruwaa.ibrahem

the limma gene set tests such as camera, romer etc to my RNAseq dataset which I have analysed in DESeq2.  Am I right in thinking that the rlog transformed counts are the appropriate matrix to pass into these functions...to pass a DGEList object to camera (edgeR::camera.DGEList) so I suppose a feature request for DESeq2 would be something similar, but certainly some guidance in the docume…

deseq2 edger limma romer camera

updated 10.5 years ago • phil.chapman

Hello Im trying to do an RNA seq differential expression analysis using DESeq2 by doing a likelihood ratio test The DESeq2 manual states " The likelihood ratio test can be performed by ...providing

deseq2 likelihood ratio rna seq wald test

updated 6.5 years ago • adeler001

I have got an Apple MacBook Air M1 with R version 4.2.2. I installed DESeq2 but I can not run it. How could I resolve this error? I tried run DESeq2 with this code: ```library("DESeq2")``` I got this error: ```Loading...anyMissing, rowMedians Error: package or namespace load failed for ‘DESeq2’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/Users/thuso…

DESeq2 apple-m1

updated 3.3 years ago • Norbert