Hi,
the default DESeq2::DESeq(betaPrior=TRUE) parameter seems to prevent finding single highly significant genes (e.g. inserted into a random...data set):
<pre>
library(DESeq2)
ex <- makeExampleDESeqDataSet(n = 60000, m = 10)
design(ex) <- ~ condition
spikeIn <- matrix(as.integer(c(5,0,177,69,119, 57842...lt;- DESeq(ex, modelMatrixType = "standard", parallel =…
Order by: Relevance
Hello, usually I load the condition table from a table in order to have a data frame with a column called condition that I put in the design formula:
<pre>
dds = DESeqDataSetFromTximport(txi, cond, ~condition)</pre>
I do not create a factor of the column condition ad I usually use contrast in order to do choose the comparisons that I need.
Is it correct do in...formula:
<pre&g…
updated 8.6 years ago • ribioinfo
x=counts(dds), cIdx=rownames(dds), k=10, scIdx=makeGroups(dds$condition))
This results in the first 8 latent factors being correlated with multiplexing runs, and factors 9 and 10 nicely separating known haploid from...x=assay(vsd), cIdx=rownames(vsd), k=10, scIdx=makeGroups(vsd$condition), isLog = TRUE)
Here, the first 6 latent factors separate a few strong phenotypes, while factor 7 captur…
RSEM to count the reads. I used fastq files as input for RSEM not bam files (sorted by name). In the DESeq2 manual it says, name sorted bam files are necessary to run the analysis for paired end reads, So can I use the RSEM output...that I have, for DESeq2 or not?
Thank you so much for your time and help.
Deepti
I like to do a PCA on an expression matrix . How could I (or can I
even)
incorporate categorical factors into the mix. I've seen PCAs that
allowed
for factors along with numerical measures, but am unsure how it would
fit in...Is this feasible?
The reason I ask this is that I like to see how much of and influence
each
factor is making on each sample.
Thank you.
-
Regards,
Sherosha
[[al…
updated 16.9 years ago • Sherosha Raj
Hello I'm doing an rna seq differential expression analysis using DESeq2 I did the read counting using **FeatureCount** but didn't normalize the read counts after. I just wanted to confirm if I...interpreted the DESeq2 manual statement correctly ? Is it saying I don't need to write a command for DESeq2 to do the read count normalization...in my script because DESeq2 already does it automat…
Dear all,
I have a question regarding the consideration of the biological replicates inside the design formula of DESeq2. We performed 2 different approaches, one being (design=~condition) and the other (design= ~replicate + condition) (see Metadata in picture 1) and found out that there were significant variations in number and padj value of DEG detected.
![colData][2]
Since PCA plot s…
updated 6 months ago • Christian
Hi I'm having an issue with DESeq2 results. I'm working with 2 cell lines from different patients and originally I created a .csv excel file with both...SerialParam())
\#Add column as listed in sample.csv
colData(se)$group= sample$group
\#Run DESeq2 with variables
library(DESeq2)
dds<-DESeqDataSet(se, design=~group)
dds<-DESeq(dds)
\#Results that contr…
Hi, is it possible to remove batch effects with ComBat and then to do a differential analysis with DESeq2? If yes, what are the steps to do?
Thank you
to account for the several batches, as well as the patient origin of these cells.
I have created factors for all three variables, but I am not sure if these are necessary.
responder_group <- factor(meta_data$Responder_status...patients <- factor(meta_data$Patient_id)
batches <- factor(meta_data$processing_date)
Here's the two design matrices I saw most frequ…
updated 5.8 years ago • msveldhuis96
Hi,
I am writing a post because I encountered an interesting question when using DESeq2.
I want to analyze RNA-seq data gained from samples of two groups: control and treatment (inhibitor of a kinase). I want...the differential count. So I am writing to ask about the possibility of reporting these numbers in DESeq2. I believe it would help a lot of downstream lab work and benefit future biomedi…
updated 3.0 years ago • Yongqing
Hi everybody,
This is a quick question regarding the DESeq2::sizeFactors() function.
To my knowledge, and I hope I am right here, this function prints out the size factor table calculated...by the DESeq2::estimateSizeFactors() function, or can be used to assign a size factor table to a DESeqDataSet.
This is not working for...object = dds)
using 'avgTxLength' from assays(dds), correcting…
updated 6.9 years ago • Ben
V-0 samples and looking for the effect of drug (~ Drug)
2 - Using all of the data, creating a new factor of DrugDose (e.g, A\_0.1, A\_0.3, etc) and looking for the effect of that (~ DrugDose).
In the first case, to get all dose to control
DESeqDataSet object, and normalized the counts using the "median ratio method":
```
counts_sp1 <- DESeq2::counts(dds_sp1, normalized = TRUE)
counts_sp2 <- DESeq2::counts(dds_sp2, normalized = TRUE)
```
Then, I used `biomaRt` to retrieve...969.89 | 858.79 |
```
Lastly, I used the count matrix including both species to compute size factors again and then divided the count v…
updated 5.4 years ago • fl
nullDist", adjMethod="BH", gsc=gsc, gsSizeLim=c(5,Inf))
with:
fc\_xxx = log2fc of genes (ouput deseq2)
pval\_xxx = the p-values (output deseq2) or should we use the adj p-value from deseq2?
This seemed to work, can anyone confirm
updated 9.2 years ago • simonp.snoeck
I'm comparing results generated by two tools that internally use DESeq2 but yield quite different results. The only relevent difference is that one tool calls DESeq with modelMatrixType...expanded".
Both are fitting the same model (`` ~ GROUP) ``, where group is a factor with four levels, and specifying a contrast in `` results ``using the names …
updated 10.1 years ago • Gregory Warnes
gt; library("DESeq2")
Error: package or namespace load failed for ‘DESeq2’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
there
Hello,
I am using DESeq2 to perform LRT analysis of a multi-treatment experiment, like an ANOVA. I have 5 different conditions, each with 4 replicates...Hello,
I am using DESeq2 to perform LRT analysis of a multi-treatment experiment, like an ANOVA. I have 5 different conditions, each with 4 replicates, and would like to generate a single p-value that indicates difference am…
Hello everyone,
I have an experiment with a 2 x 2 factor design, with condition having two levels (N vs NN) , and treatment having control (C) and stress (S) levels. I want to analyze...I run
```r
res1 <- results(dds_pol_nod, name = "conditionNN.treatmentS")
```
where by reading DESeq2 vignette and ?results example 3, I interpret that "conditionNN.treatmentS" means analyzing if the …
updated 3.6 years ago • mmartinez
Would anyone please help me to fix this error when installing DESeq2? I looked for the same error on the Internet but could not apply to my case. Thank you!
```r
BiocManager::install('DESeq2')
```
Warning...genefilter’ had non-zero exit status
2: In install.packages(...) :
installation of package ‘DESeq2’ had non-zero exit status
updated 3.4 years ago • doanc2
Hi everyone.
I have a problem with DESeq2 counts in r.
when I use this code:
raw_readcount <- fread("raw read counts.txt", header = TRUE, sep = "\t")
design <- fread("Design.txt...Hi everyone.
I have a problem with DESeq2 counts in r.
when I use this code:
raw_readcount <- fread("raw read counts.txt", header = TRUE, sep = "\t")
design <- fread("De…
updated 3.6 years ago • ali reza
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…
My script was working a month ago, but now it's not. I'm struggling with getting my DESeq2 analysis working. Here's what I'm trying to do:
factorNames <- c("Experiment", "Line");
dds <-
DESeqDataSetFromMatrix(count.mat...produce the error)
Reordering my library declarations at the start of my script:
library(DESeq2); library(tidyverse); library(magritt…
updated 6.0 years ago • David Eccles (gringer)
Hi Mike,
I wonder how did you calculate the "baseMean counts" in the output of DESeq2. I looked the Genome Biology paper and additional files, it seems you used mean counts or mean expression there. If you...gene lengths (RPKM), but I didn't input anything related to gene lengths in the analysis with DESeq2. Did you estimate gene lengths or just using a same length for all the genes or should it…
updated 10.1 years ago • zpingfeng
I'm trying to adjust batch effect using `deseq2 limma::removeBatchEffect` and also `Combat-Seq`. With limma version, I can clearly see the batch effect is removed, where...correction with limma::removeBatchEffect][1]
But from this `limma:removeBatchEffect` function of `DESeq2`, I don't get any batch corrected counts or TPM / FPKM expression data. I need this TPM for performing ssGSEA and various…
updated 2.7 years ago • vk
<div class="preformatted">Dear mailing list,
I recently found out about the new DESeq version and am currently in
the process of switching my pipelines to use it. You included some
sweet new features and those may simplify my life a lot. Now my
questions relate to the output tables bearing the final differently
expressed genes.
1. Is there a plan to reintroduce the old DESeq 1 column…
have been sequenced. So I have only one level, one condition. But I have n=551 patients. Can I use Deseq2 to see a differential expression in my patient cohort even if I have no control. Only one level (one condition= cancer...I have use Deseq2 in the past but it was for a study of difference between cell treated against control.
Here I have no control ...
Is Deseq2
updated 8.8 years ago • cardin.julie
subset for my cell-type of interest, creating a single Deseq object. Then, create an "interaction" factor merging the origin Study (GSE1, GSE2) X cell Condition (Fed, FD) variables. I would use the design=~interaction.
This way I...get the average of the results of the previous comparisons? or is there a better way I could tell Deseq2 to give me the average of such comparisons in a single outp…
updated 6.8 years ago • baldissera152
Hello,
I have tried to understand how DESeq2 calculates the Log2FoldChange. I extracted the normalised counts from dds like below, calculated the mean of treated...log2(treated/control)`. But the log2FC I get using this method is different the one I get using DESeq2. Moreover, it seems like log2FC reported with DESeq2 is calculated based of difference of mean treated and control...CTRL1 mean_tre…
and I'm trying to install packages that I need for RNA sequencing analysis. I would like to use the DESeq2 package and I'm trying to install it on my Mac computer. This is the output that I get. Any suggestion to fix the ____problem...Thanks!__
<pre>
> install.packages("DESeq2")
Warning in install.packages :
package ‘DESeq2’ is not available (for R version 3.3.3)
&…
Hi everyone,
I'm fairly new to coding and I've recently run into some trouble with my for loop for DESeq2 in R. Apologies if this is a dumb question!
To give some background, I have many different columns in my colData that I want...everyone,
I'm fairly new to coding and I've recently run into some trouble with my for loop for DESeq2 in R. Apologies if this is a dumb question!
To give…
Hello,
I'm currently trying to use Deseq2 but I'm getting confused with some of the conditions.
I have multiple individuals that are either Sick or Healthy (that...dds
design(ddsMF) <- formula(~ family + condition)
print('Running DESeq on multi-factor data.')
ddsMF <- DESeq(ddsMF)
resultsNames(ddsMF)
resMF <- results(ddsMF, contrast=c("c…
updated 5.2 years ago • benoit.j.kunath
Hello, I have about 150 human genes. I want to build a transcription factor-gene network so I need to find which TF binds to which gene?
Is there any bioconductor package for finding possible...Hello, I have about 150 human genes. I want to build a transcription factor-gene network so I need to find which TF binds to which gene?
Is there any bioconductor package for finding possible transcripti…
updated 8.6 years ago • hkarakurt
Hi,
DESeq2 error while running, please help!
**Installed**
conda create -y -n test.DESeq2 python=3
conda activate test.DESeq2
conda...install -y bioconductor-DESeq2
**To Run**
$ cat counts.txt | deseq2.r 3x3 > results2.csv
ERROR Error: package or namespace load failed for 'DESeq2' in dyn.load...DLLpath, ...): unable to load shared object '/Use…
Hi all,
I'm currently doing differential gene expression analysis on Nanostring data.
For this I'm using the package NanostringDiff.
I try to detect the effect of a treatment vs the absence of treatment on a set of ex vivo biopsies samples.
Due to strong heterogeneity between individuals, the "sample" effect is much stronger than the "treatment" effect (gene response is close between treated …
updated 7.0 years ago • Guillaume Robert
Hello, i have this code and i want to put to the subject the first sequence from my fasta file but i don't know how to do it.
Thank you
library(TFBSTools)
library(JASPAR2020)
library(Biostrings
Hi,
I am running DESeq function in DEseq2 (version 1.16.1) and it's taking too long . I had it running over night and it's still not done.
I am thinking it's because...Based on previous post (about 3.3 years ago), I also tried converting all metafile components to factor. Thanks for your input in advance!
dds.adj2<-DESeqDataSetFromMatrix(countData = hg38.…
the read counts are already collapsed to gene-level, resulting in a matrix with gene names in the first column (e.g. TP53, A2M), genome-coordination in the second column (e.g. "chr17_7661779_7687550_-") and raw counts in the rest...the conclusion that the best methods for normalization for correlation analysis are edgeR's TMM and DESeq2 normalization. Based on the other posts, I think the followi…
Hi,
I have had problems installing the "DESeq2" package. I am new to working in R and have had a lot of problems installing DESeq2 package in R. I have tried several installation
updated 5.3 years ago • price793
two conditions (WT and KO) across multiple tissues in terms of number of significant genes using DESeq2. Some tissues had good distributions of p-values (0-enriched) but some showed skewed to right where I could adjust using...to all the tissues (including the tissues with good distribution of p-values obtained directly from DESEq2) and compare the number of significant genes (alpha<0.01) …
I am a frequent user of DESeq2 (when I don't have technical replicates of my libraries). When I have technical replicates I usually go for Sleuth.
I have...seen people that conduct analysis in DESeq2 with ONLY two either biological or technical replicates.
We always include at least three samples in each group (experimental...and control), and ideally more.
Is a DESeq2 comparison of two groups…
updated 7.8 years ago • jovel_juan
I'm trying to use DESeq2 to perform something like a one-way ANOVA on 3
groups of samples. I've seen references to DESeq2's capability of
performing...http://seqanswers.com/forums/showthread.php?t=16539
However, I can't seem to find anything in DESeq2's manual about how to
do this. I have my data inputted successfully, and I've been able to
perform pairwise comparisons...using D…
I am trying to use the Noiseqbio method in order to compare the results with other methods (edger, deseq2 and limma+voom).
I obtain very similar results for edger, deseq2 and limma+voom but i obtain completely different results...pvalue of 0.05 and a log fold change of 1.
my code :
mydata = NOISeq::readData(data = countsTable, factors=conditions)
myTMM = tmm(assayData(mydata)$exprs, long = 10…
updated 7.7 years ago • Aurora
How can one use `DESeq2 v. 1.18` from the latest `Bioconductor v. 3.8`?
I need to use one package that works reliably only in `Bioconductor 3.8`, but...all my previous analysis was done using `DESeq2 v. 1.18`, which is from older Bioconductor release.
Thanks
updated 6.8 years ago • gtechbio
Hello,
thanks for developing an amazing tool like DESeq2 and having it available to the scientific community. I am new to RNAseq analysis. I have read the vignettes and I have...in the design or use sva to remove hidden batch effects? If I use sva, shall I have the confouding factors in my initial design formula and then change according to sva (I can use as reference the code given in the vig…
updated 4.2 years ago • m.glymenaki
Hi I have done a DESeq2 DGE analysis and it showed an error when I was using ashr shrinkage
```
using 'ashr' for LFC shrinkage. If used in published...1.14601e-18); attempting approx solution
```
I assume that stems from co-linearity of some of the factors? Is there any fix? May I ask if the result is trustworthy? And if I am going to use it is there anything I should be careful
the 15 combinations I have triplicates (in total 45)
If I understood it correctly both edger and deseq2 works with this interactions terms to combine multiple factors (They use different commands, but the interactions...Placebo.0h),
If I want to test for changes between treat and ctrl for each TP should I use the first contrast and do this (after combining the columns `treatment` and `day` …
updated 6.9 years ago • Assa Yeroslaviz
I've been using DESeq2 (v1.14.1) for some time (in R v3.3.3 on Mac OS 10.10.5), but now get following error when loading DESeq2 :
```
Error in library.dynam...I've been using DESeq2 (v1.14.1) for some time (in R v3.3.3 on Mac OS 10.10.5), but now get following error when loading DESeq2 :
```
Error in library.dynam(lib, package, package.lib) :
shared object ‘stringi.so’ not found
Error: p…
updated 6.1 years ago • sagharib
opinions/criticism.
**In short, I can't figure out if I should use all my data or half my data in DESeq2 for calculating the size factors and estimating dispersion etc. i.e. when are the samples 'too different' and including...of interest as well. There are multiple genes that are only expressed in clone1 or in clone2, which DESeq2 won't include in normalization, but could be important for a clo…
updated 4.9 years ago • Kelen
Hi,
HTG EdgeSeq assay provides a toolkit doing differential expression by DESeq2. I compared results coming by this software and when I am doing DESeq2 in R version 3.5.1 manually like
dds=DESeqDataSetFromMatrix...expression analysis has been completed using the DESeq2 package (version 1.14.1) available from Bioconductor. The DESeq2 package provides methods for estimating and testing..…
updated 6.2 years ago • Fereshteh
Hi,
I have run my initial analysis without filtering for low-expressing genes, given DESeq2's independent filtering procedure. Due to the low number of significant genes returned when using an FDR, we have opted...Hi,
I have run my initial analysis without filtering for low-expressing genes, given DESeq2's independent filtering procedure. Due to the low number of significant genes returned wh…
updated 3.1 years ago • erbrocato
during this pandemic. I have a few questions that hopefully can be addressed here. I am running both DESeq2 and edgeR on two experimental designs I have (one with paired samples and one without). I assembled a de novo transcriptome...file to perform differential expression analysis. I have successfully run tximport on this data for DESeq2, and I was able to push the program all the way to the end…
updated 5.6 years ago • hollandademello
Dear [Michael Love](https://support.bioconductor.org/u/5822/):
I used fpkm(dds) form DESeq2 R package to calculate fpkm , the progress did not show any error.
The I summed all gene's fpkm value belong to 1 sample...Dear [Michael Love](https://support.bioconductor.org/u/5822/):
I used fpkm(dds) form DESeq2 R package to calculate fpkm , the progress did not …
Hi, I'm trying to update my DESeq2 package. I uninstalled the old package using remove.packages("DESeq2") then install as normal using biocLite. However...it keeps installing the older version of DESeq2 1.2.10 instead of the newest version. What am I doing wrong? Please help!
Zach
controlling the effect of "Mother" (litter).
I have 8 different groups and 11 mothers. Both were factored.
With a design like this:
```
dds = DESeqDataSetFromMatrix(countData = cts_filtered,
colData = colda_t,
design = ~ group + Mother...must be removed.
Please read the vignette section 'Model matrix not full rank':
…
updated 3.1 years ago • TzuChiao
analysis and I just wanted to verify that it is fine to use the non-integer counts with edgeR and DESeq2. Years ago, we needed to round the decimal counts from e.g., cuffdiff, but the tximport vignette implied the non-integer...support.bioconductor.org/p/65890/\#65938 and https://support.bioconductor.org/p/45695/, the first of which has Steve Lianoglou asking for a separate post to highl…
I have just upgraded my R to 3.2, bioconductor to 3.1 and then installed the latest DESeq2 package and now a DESeq analysis that used to work keeps failing with the same error. Here is what I have been doing:
<pre...normalized=TRUE)
> filter<-rowSums(nc >= 15) >= 3
> ddsf<-dds[filter,]
# run DESeq2
> ddsf<-DESeq(ddsf, parallel=T)
u…
I'm analysing an RNA-Seq datasets with edgeR and using calcNormFactors to estimate normalisation factors. In one of my experimental groups all samples have normalisation factors above 1, while in another group all samples...have normalisation factors below 1. Library sizes do not vary systematically between the groups.
What could be an explanation for this pattern
updated 7.7 years ago • maltethodberg
is the bamcoverage of such a gene.
![Read Coverage][1]
And below are the rpkm estimated by Deseq2 (gene level) and StringTie-ballgown (transcript level) - commands used are at the end of this post :
AMP (blue track) DLM (green...track)
fpkm by Ballgown 40.6 5.1
fpkm by Deseq2 21.3 …
updated 6.0 years ago • JindrichK
Hiya,
I am finding that if I am inputting my data in one count matrix and calling to contrast two different treatments from the four (each with 5 sample replicates) using the contrast function in DESeq2 that I get different differential expression results to that if I look at the samples using the automated trinity DE analysis pipeline using DESeq2. I am assuming that this is beca…
updated 8.8 years ago • bekah
Recent ...
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