analyses or plotting on the residuals.
Is there a way to do something similar directly with DESeq2? I.e., not via using normalized and log2(x+1)-transformed in a separate lm().
Best regards,
Marc
Order by: Relevance
I am analyzing a time series of a metatranscriptome. In metatranscriptomics, we have to do the regular normalizations found in RNA-Seq (ie. gene sequence length, and sample-differences in total expression). However, there is an additional normalization required to account for changes in species abundance.
I would like to analyze differences in species-level transcript abundance, so I've done all…
updated 8.4 years ago • jspmccain
lt;- relevel(dds$condition, ref = "wt")
If I am using the same string of code but, I merely duplicate my folder with aligned files (e.g. just wt and wt-treated) together with another sample table with just the selected
updated 6.6 years ago • Mozart
nest the replicates within the main groups OR set the replicates as a random effect when running the DESeq2. I am not particularly interested in differences between the replicates (we would like to assume that there are none
updated 10.6 years ago • Silva
I came across an issue when trying to import RSEM files into DESeq2 according the [online tutorial](https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html
updated 8.9 years ago • falkohofmann
two different count matrices from salmon results, then merge them and import the final one in deseq2 (DESeqDataSetFromMatrix) considering to include in the final design formula the experiments from where the samples
updated 5.2 years ago • sconosciuto
I use deseq2 to compare the transcriptomic signatures of 3 cell types composing the same tissue (A, B, C). The object "res" returns only
updated 6.8 years ago • gilles.charpigny
div class="preformatted">I have a data set which pretty much duplicates the experimental design
of one of the limma examples, so I am using that with great results
:-D
There is one difference...though - the limma example has no duplicate
spots, whereas my design does. So I did two runs of limma, one to
find
differentially expressed spots, the other to...differentially
expressed genes (I assu…
Since `DEXSeq::estimateDispersions()` and `DESeq2::estimateDispersions()` are often the most time-consuming step of the two pipelines I was wondering if it was possible...to share the result of this between a (naturally paired) DTE and DTU analysis using DESeq2 and DEXSeq respectively or if they are indeed different?
Cheers
Kristoffer
expression across/within sample groups. For now we have just followed the basic documentation of DESeq2. We used plotDispEsts which can indicate if the data works well with DESeq2 or not. The plot looks like this -
![plotDispEsts...output][1]
From what I understand, this indicates that DESeq2 can work for the data, however why are there some gene-est which are at the lower left corner? Is it…
Hello all,
I have a large RNA-seq dataset that I am trying to run WGCNA on. The data set has many variables including (including 3 brain regions, 3 ages, sex, 2 genotypes.) I have been advised to use Deseq2 normalization for these samples prior to doing WGCNA.
I am struggling with two aspects.
1) I assume I am not actually doing...including (including 3 brain regions, 3 ages, sex, 2…
Say I have three samples with a simple design formula ~condition:
sampleA - control
sampleB - treatment (replicate 1)
sampleC - treatment (replicate 2)
DESeq2 returns one fold-change for control vs. treatment, but it is possible to consider separately control vs. treatment rep...condition:
sampleA - control
sampleB - treatment (replicate 1)
sampleC - treatment (replicate 2)
DESeq2 returns…
updated 4.5 years ago • P1000
Is it possible to conduct a linear regression analysis in DESeq2, where one could get a slope, r-squared, and p-value? Based on this post (https://support.bioconductor.org/p/88254/) it...Is it possible to conduct a linear regression analysis in DESeq2, where one could get a slope, r-squared, and p-value? Based on this post (https://support.bioconductor.org/p/88254/) it looks l…
updated 8.4 years ago • chimeric
<div class="preformatted">Hi,
I wanted to use a normalised read count matrix from EDAseq downstream
in DESeq2 analysis. I am not very clear on how to do so from the
vignette.
Following are the steps I followed -
## EDAseq - normalising count matrix by GC content
> dataWithin <- withinLaneNormalization(data, "pct_gc", which =
"full")
> dataNorm <- betweenLaneN…
updated 11.5 years ago • Guest User
DNA synthesis.
Can I just use the functions related to DNA synthesis (subset table) to do the DESeq2 analysis or I have to use the whole dataset and later found which over-representative functions relative to DNA synthesis
updated 8.8 years ago • Pet Chiang
I would like to visualize how good is the fit of a model estimated using DESeq2, for instance by plotting the data along with the corresponding predicted values. Is there any equivalent of the \`predict
updated 9.5 years ago • philippe.veber
objectives was to identify differentially abundant genes across my sample groups, which I did using DESeq2
I am wondering if its also possible to do some qualitative testing, based on the presence-absence of a gene and quantify
to investigate changes in circRNA expression in concert with rates of RNA-editing. For my initial DESeq2 analysis I combined linear read-counts generated from the Rsubread function ```featureCounts``` with circRNA counts...and DCC. The combined count matrix was analyzed with the standard workflow detailed in the DESeq2 tutorial.
I then used the SPRINT toolkit to detect RNA-editing sites and e…
updated 6.2 years ago • maxhenryhills
the control consortium?
To answer these two questions I would like to know if it is possible with DESeq2 to block one of the 2 variables, for example comparing for the consortium of strain n°1 the differents pH points to the...to keep only the results of counts of genes corresponding to the consortium of strain n°1 and use DESeq2 with a single variable, the pH?
I tried some models like :
…
In a [previous question](https://support.bioconductor.org/p/85486/) I asked about how DESeq2 could be used to take the effects of sequencing from knockout (KO) tissue. This is possible by using interactions. If...In a [previous question](https://support.bioconductor.org/p/85486/) I asked about how DESeq2 could be used to take the effects of sequencing from knockout (KO) tissue. This is possible b…
updated 9.4 years ago • snamjoshi87
I have 15 samples completed using miRDeep2 but need to upload files to R studio to get started on DESeq2. How do I input the files so I can start pre-filtering before the differential expression analysis
updated 5.8 years ago • ljbond
Hi all!
Using DEseq2 (v 1.30.0) I try to analyze a "complex" data set with 2 factors (A and B) harboring different levels.
Factor A (named hereafter...Hi all!
Using DEseq2 (v 1.30.0) I try to analyze a "complex" data set with 2 factors (A and B) harboring different levels.
Factor A (named hereafter "line") has two levels (infected/non-infected) and factor 2 (named hereafter "group") has 4…
updated 5.0 years ago • lessismore
to quantify the reads. Therefore, I would like to normalize the reads in the different sample using DESeq2. May I know if there especial consideration that I should take before doing it.
I mean I did not find anything related...to EXOM seq in the DESeq2 vignettes.
Best
AD
I am working on analyzing a dataset using DESeq2. The main goal of the analysis is to compare the gene expression profiles between treated and untreated group. Since...the patients about their heart disease status.
Now my question is what is the best way to write deseq2 design and contrast in order to extract something like, what are the differences between treatment groups for men
updated 6.6 years ago • hrishi27n
Hello everyone,
I am trying to install DESeq2 package in r version 4.0.2 but it doesn't work. I have searched a lot on different pages but I couldn't find a solution...BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("DESeq2")
And the errors:
* installing *source* package ‘RCurl’ ...
** package ‘RCurl’ successfully unpacked and MD5 …
updated 5.3 years ago • armin.shahpari
Hi everyone,
Is there any script that links DE genes identified by DEseq2 directly to ReactomePA for Functional enrichment analysis?
thanks much
 
updated 9.3 years ago • ta_awwad
Hi everyone,
I am new in bioinformatics and when I try to use DESeq2 for my counts and further downstream analysis, I am faced with this problem.
dds <- DESeqDataSetFromMatrix(countData
updated 2.3 years ago • Beyza
Hi ,
I recently installed the latest version of DESeq2 (VERSION 1.6.0) and upon running the command DESeq(dds), I receive the following error:
Error in ncol(mcols(dds)) :
 
How does DESeq2 account for the dependency between samples in repeated 16S data, for example, relative abundance for samples from
updated 6.0 years ago • jperin
Hoping I can get some help. I have been using DESeq2 for several months now on several different projects (I manage a NGS core). For most of these projects, the samples do...Hoping I can get some help. I have been using DESeq2 for several months now on several different projects (I manage a NGS core). For most of these projects, the samples do not
updated 8.5 years ago • gkuffel
Hello!
If I wanted to conduct WGCNA analysis following a salmon/DESeq2 workflow, would it be appropriate to use the matrix generated after applying the vst function on the dds object? Something
html?sid=9574bcdf-13ab-47a0-909b-1dfbb4dcf9ee>
It seems that DESeq is better than DESeq2. What is yours opinion (expecially from the authors)?
Thank you.
Riccardo
1) illuminahiseq_rnaseqv2-RSEM_genes*** file is the most suitable for subsequent analysis with DESeq2 imported through ***tximport***.
There are 3 columns associated with each samples in the **1) illuminahiseq_rnaseqv2-RSEM_genes...it is estimated counts because data not in integer format***) column will be more appropriate for DESeq2 analysis imported via **tximport**.
If anyone please co…
updated 5.6 years ago • J. Smith
have to divide into 2 batches for sequencing. Following sequencing, I used Tophat2-featureCounts-DEseq2 pipeline to analyze them. My question is: should I merge the FeatureCounts result into one file as the input for...DEseq2? Is it OK that I run the pipeline for each batch of samples, generate the DE results (Condition vs control) and then compare...F.3</td>
<td>ConditionF&…
updated 9.4 years ago • EJ
R version to 3.4.0 on a mac, after successfully re-installing sundry bioconductor modules, including DESeq2, when I load DESeq2 I get the following:
library("DESeq2")
Loading required package: S4Vectors
Loading required package...masked from ‘package:base’:
apply
Error: package or namespace load failed for ‘DESeq2’ in dyn.load(file, DLLpath = DLLpath, ...):…
updated 8.7 years ago • afreedman405
Dear all!
Sorry for yet another question on pre-filtering and DESeq2, but I didn't find anything related in the support pages... Now to my question:
I know that DESeq2 does a wonderful job of automatic...interferes or violates the assumptions of the dispersion estimation (or any other assumption) in the DESeq2 model (Also considering that the pre-filtering in DESeq2 takes place after calculatio…
updated 10.7 years ago • Johannes Rainer
Hi Michael,
I got some question about the tutorial of DESeq2 and I was wondering if you could help me in:
1) normalized metric you use in Deseq is not referring to RPKM or TPKM, but: "counts
updated 6.6 years ago • santamariagianluca
ind+grp+cnd+grp:cnd
~grp+grp:ind+grp:cnd
~grp+cnd+grp:ind+grp:cnd
After reading the DESeq2 manual and forums I still did not understand the differences.
My experiment design is:
GROUP CONDITION ind.n
s1 CONTROL
updated 5.5 years ago • aec
three biological replicates) be represented on the plot, instead of all three replicates.
In DESeq2 package I use:
library(ggplot2)
data <- plotPCA(rld, intgroup=c("clade", "strain"), returnData=TRUE)
percentVar
in two different condition. Thre was quality issue with the extrected RNA samples. Later i ran deseq2 normalization (by first using estimateSizeFactors and then variance stablizing transformation (vst) transformation...After the full deseq2 analysis i can see huge difference in replicate of one sample (many of the genes are highly expressed in one replicate...if my steps are correct (though i fo…
updated 4.4 years ago • Shail
Hi
I am using Deseq2 for Differential gene expression analysis. I have two controls ( but they are not technical replicates) and one patient...I designed the experiment with two controls together. I was wondering what Deseq2 does when two controls are taken together. Does it takes an average of the two controls.
Many Thanks
Tanya Singh
Dear DESeq2 team,
I am currently using DESeq2 (v1.12.0 under R 3.3.0) to analyse some processed single-cell RNA-seq data, and the...Dear DESeq2 team,
I am currently using DESeq2 (v1.12.0 under R 3.3.0) to analyse some processed single-cell RNA-seq data, and the data's inherent noisiness is leading to many genes having many values detected as outliers (eg >3k genes…
updated 9.6 years ago • aatsmith
Hi, I'm using DESeq2 to identify differentially affected histone modifications in cells from control and treated human populations...but the background is a little higher when the reads were mapped without the threshold.
DESeq2 yielded a handful of significant hits (BH-corrected pvalues <0.05) using the count table made from data mapped in...first way (no mapping threshold), bu…
updated 11.0 years ago • David Auble
Hi,
I am trying to use DESeq2 to analyze an experiment where I have read counts from individuals assigned to 1 of 2 groups, and each...by-time interaction). I have primarily been using the webpages "Analyzing RNA-seq data with DESeq2" and "RNA-seq workflow: gene-level exploratory analysis and differential expression" to figure out the appropriate...ind distin…
updated 8.2 years ago • jpkarl
Hi,
I have a question about the results of DESeq2. Usually, I use q-value<=0.05 and |FC|>2 as the criteria to screen differentially expressed genes. If I want to identify
updated 5.8 years ago • wangy660
Hello,
I am using DESeq2 for analysis of RNAseq data. I would like to ask you about the design in the DESEq2 formula. I have tissue from animals...with all the groups I am going to need?
```
coldata<-read.csv('metadata.csv',header=TRUE,row.names=1,stringsAsFactors = FALSE)#a table with information about the samples
head(coldata)
str(coldata)
coldata$Treatment
updated 4.1 years ago • m.glymenaki
control probes using package illuminaHumanv4.db Version:1.26.0
Error in value[[3L]](cond) : duplicate row.names: 200647550006
AnnotatedDataFrame 'initialize' could not update varMetadata:
perhaps pData and varMetadata
I am trying to re-run a couple of new comparisons using DESeq2. I have previously used this script but something must have changed or updated in the last couple months that is responsible...C", "D", "A", "B")
#technical replicates
coldata=as.data.frame(cbind(location, temp, individuals))
row.names(coldata) = names(countData)
coldata
# ----------Construct data object ----------------------------…
updated 5.1 years ago • Amy
a bit of trouble understanding how `` lfcThreshold `` parameter of the `` results `` function of `` DESeq2 `` affects the p-value. Imposing a stricter `` lfcThreshold `` reduces the number of significant results, which makes sense...1] : 39, 0.054%
low counts [2] : 8476, 12%
(mean count < 0)</pre>
I've looked at the DESEq2 paper, the vignette, and the workflow, and cannot fi…
updated 8.2 years ago • Russ Fraser
Hello, I am posting to report what I think is a bug in an error message in DESeq2. I suspect that `DESeqDataSetFromMatrix` misdiagnoses the input type when the user passes a factor, reporting to them...which I reproduce and inspect the issue, or a Git repo [here](https://github.com/sweeney-th/possible-deseq2-bug).
edit: there is a better-formatted version on the PDF report [here](https://drive…
updated 5.7 years ago • thadryan
Hello,
I suddenly got problem installing DESeq2 and would really appreciate help.
The issue seems to be packages cache, data.table and xfun that can't be updated to...Hello,
I suddenly got problem installing DESeq2 and would really appreciate help.
The issue seems to be packages cache, data.table and xfun that can't be updated to their...version.
I use RStudio 1.4.1106.
I start the installat…
updated 4.6 years ago • kvitt_silver
Hello,
Since yesterday I am facing an error uploading deseq2 package that has been installed for a long time and worked perfectly fine until yesterday. the error is
Error: package...or namespace load failed for ‘DESeq2’:
objects ‘rowSums’, ‘colSums’, ‘rowMeans’, ‘colMeans’ are not exported by 'namespace:S4Vectors'
I have restarted the R session
Hi all,
I have some question about the lfcshrink function of DESeq2.
When analyzed using the unshrinkage method in DESeq2, the fold change was overcalculated (Log2FC= ~30), so we are trying...to apply the shrinkage methods in DESeq2. There are three methods (apeglm, ashe, normal) introduced in the DESeq2 vignette, and among them, I would like to use the
for sex OR better explained by disease state and sex combined?
<pre>
(coldata = data.frame(row.names=colnames(countdata), disease, sex))
dds = DESeqDataSetFromMatrix(countData=countdata, colData=coldata, design=~sex
updated 7.4 years ago • agdif
Hello Everyone,
I am in a big problem, when I am running the DESeq2, the genes which are up and down-regulated or at all differentially expressed, some of them are not appearing in my result...and suggestion to find the problem? also, I am sharing the commands which I use for running the DESeq2. please let me know what is the problems? I would really appreciate your help in my this tough situ…
updated 3.2 years ago • Maryam.sed1400
Hello,
I have the StringTie output files and need to run DGE using DESeq2.
I ran the following code:
```library(tximport)```
``` <- read_tsv("t_data.ctab"[1])```
```tx2gene <- tmp[, c("t_name", "gene_name")]```
With that I...Hello,
I have the StringTie output files and need to run DGE using DESeq2.
I ran the following code:
```library(tximport)```
``` <- r…
updated 4.8 years ago • ahmesalama
HI everyone,
I'm running DESeq2 to identify genes that are differentially expressed between two general phenotypes: fruits and vegetables. Here...HI everyone,
I'm running DESeq2 to identify genes that are differentially expressed between two general phenotypes: fruits and vegetables. Here's my design:
```r
general specific batch
===================================…
Hi everybody,
I am producing right now a strange plot while running the DESeq2 workflow when running the command `` lfcShrink `` on the DESeqDataSet object (after running the `` DESeq `` function).
I assume...object=dds,...) ``, right plot showing `` lfcShrink(dds_calc,...) ``
Both plots plotted using `` DESeq2::plotMA(...) ``.
<img alt="" src="https://i.imgur.com/RNTWlht.png" st…
BasePairTech. From what I gathered, it runs a gene count with STAR and it feeds the results to DESeq2 for the following experiments:
- 6h vs 0h
- 18h vs 6h
- 24h vs 18h
- 48h vs 24h
- 84h vs 48h
- 1 vs. the rest for all samples.
I understand...the DE experiments for two samples?
Also (very important): Which values from the gene count does DESeq2 uses from the gene count (**Gene coun…
updated 6.1 years ago • kolt.penny
Hi, I am using the DESeq2 (DESeq2_1.22.2) VST algorithm to normalize the tag count within peaks from CAGE-seq data. I want to use the VST transformed...10-20 million VST transformed read count per cell/
2) What is the pseudocount used in VST? In the DEseq2 document, I couldn't find the pseudocount for VST. Is there no pseudocount for VST?
Best regards,
Ju Heon Maeng
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