Hello everybody!
I have a question about an analysis of my polysome profiling experiment.
In my case I have to conditions (with and without treatment) and two sample types for each condition, the mRNAs bound to the monosomal fractions (only to a single ribosome, or its preinitiation forms) and mRNAs bound to polysomal fractions (more than one ribosome).
I want to compare the translation effic…
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Hi,
Is there a way to set the input in the design section of DESeq2 as variables?
The aim is that the colname chosen will be a variable that can be changed elsewhere in the script rather
updated 5.3 years ago • Matan G.
Hi everyone,
Our lab is attempting to use the DESeq2 package to perform DGE analysis with a multifactorial experimental design. Our question of interest is whether...3 controls)\* 2 conditions = 16 replicates for each of the 4 days.
<pre>
library(DESeq2)
library(RUVSeq)
# a separate dds object was created for each day by repeating these lines
condition <- f…
updated 8.1 years ago • le.alex.chang
of whether I have chosen the correct method for analyzing my
multi-factorial experiment.
I have 3 factors: factor A with 16 levels (from level0 to level15),
factor B with three levels (from level0 to leve2), and factor Sex with
two
I tried to follow the [DESeq2 tutorial](https://www.bioconductor.org/packages/3.7/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#how-to-get-help-for...deseq2), and ended up with a error.
library("pasilla")
library("DESeq2")
pasCts <- system.file("extdata", "pasilla_gene_counts.tsv...rpart_4.1-12
[58] nnet_7.3-12 compiler_3.5.0
BTW: thanks a lot to the…
updated 8.0 years ago • unamourdeswann
Hi,
I am new to RNA seq and seq data analysis.
I want to use DESeq2 to extract differential expression data for cells (from three donors) seeded on two different scaffolds (scaffold...appreciated.
Can anyone please help with design formulas for differential expression using DESeq2 for the above-mentioned comparisons.
Thank you very much in advance
Best Regards
Arun
pre>
dsgn <- "~1 + Batch + Group + Timepoint + Timepoint:Group + Timepoint:Group:X"
dds <- DESeq2::DESeqDataSetFromMatrix(
countData = countData,
colData = colData,
design = formula(dsgn)
)
dds <- DESeq2::estimateSizeFactors...dds, "poscounts")
dds <- DESeq2::DESeq(dds)
resGAT0 <- results(dds, name = "GroupA.Timepoint0.X")&l…
updated 8.5 years ago • lanhuong
I have some confusion about GAGE workflow. I understand GAGE is a type of functional class scoring tools with no preset cutoff used to identify significant genes. But I have seen several workflow/model scripts where they used the output from DESeq2 which is selected based on p-adjusted value of 0.05. Shouldn't the experimental set be the entire expression data? I guess...significant genes. But I …
updated 8.4 years ago • sup230
My experimental design consists of four groups and two experimental factors (+/+, +/-, -/+ and -/-). In addition, each group has four biological replicates (the first biological replicate of each group was taken...factor.2
[1] "contr.treatment"
</pre>
The factor.1 column represents presence/absence of factor 1 and factor.2 column represents presence/absence of factor 2.
So far, I have p…
updated 11.0 years ago • Ekarl2
Hi,
In DESeq2, while making MAPlot for an object obtained by using results function, is there a way to highlight only those genes
updated 7.2 years ago • gv
gt; e.g. the genotype.
>
> Secondly, we have the fold change of genotype 2 over 1 for the first
> time period. This is also obtained with results(dds,
> name="gen_2_vs_1")
>
> Finally are the interaction terms. For...p-values for genes which have a genotype effect which is
>>>> different than in the first time period. This test…
updated 11.4 years ago • bio2001
a paper in order to analyse the conditions myself. However the author has only provided me with the Deseq2 normalised counts. Is there a way for me to reverse calculate the raw read counts or proceed with analysis using Deseq2
hi list,
I recently upgraded my R to 3.1.2 and DESeq2 to 1.6.3. I re-run some of my code on a RNAseq experiment. Comparing to the old results (done in R 3.1.0 and DESeq2
updated 10.9 years ago • Shi, Tao
At different places (the help page for `DESeq2::plotMA()`, the apeglm vignette, and [here][1]) an s-value threshold of 0.01 or 0.005 is mentioned as a sensible choice for "false...sign" (FS) events. However, when specifying a non-zero threshold for the log2 fold change in `DESeq2::lfcShrink()`, the reported s-values refer to "false sign or smaller" (FSOS) events. In this case, the maximum possibl…
updated 6.4 years ago • Homer
class="preformatted">Hello,
I am trying to use DESeq to test for differential expression in a
multi-factor, multi-condition experiment. Factor 1 (Blocking) has 2
conditions, Factor 2 (Time) has 4 conditions and Factor 3 (exposure
each contrast to be reported in the nice framework of ReportingTools.
Now, I have 3 levels for one factor (condition) and 2 for the other one (tissue)
<pre>
ddsmf <- DESeqDataSetFromMatrix(countMatrix,
colData = data.frame(condition...pre>
Now, my best case scenario is that I specify the contrast as in the results function of DESeq2, and the corr…
updated 10.8 years ago • Federico Marini
Hi,
I am getting a new error with DESeq2 and I have no idea why as these are commands I have run a million times. I really can't understand why it's not working anymore...someone reporting this error before.
I have this object:
I am getting a new error with DESeq2 and I have no idea why! These are commands I have run a million times! I really can't understand why it's not working.
…
updated 7.4 years ago • I.Castanho
reason, one of the replicates of my htseq-count files is not normalizing correctly when run through DEseq2. I have attempted to change settings, re-map the original .fasta file, and all of my efforts still lead to the same replicate
updated 7.6 years ago • mpw183
__I have this error:__
<pre>
dHTSeq <- DESeqDataSetFromHTSeqCount(sampleTable=SampleTable,directory="TuttoCount/", design= ~ 1) #
Error in Ops.factor(a$V1, l[[1]]$V1) :
level sets of factors are different
In addition: Warning message:
In is.na(e1) | is.na(e2) :
longer object length is not a multiple of shorter object...directory="TuttoCount/", design= ~ 1) #
E…
Hi,
I'm trying to use DESeq2 to perform time series analysis like a one-way ANOVA on multi-groups of samples,but there is a obvious batch effect...Hi,
I'm trying to use DESeq2 to perform time series analysis like a one-way ANOVA on multi-groups of samples,but there is a obvious batch effect in...gt; dds<-DESeq(ddsHTSeq1,full=~ batch + condition, reduced=~1+batch, test="LRT")
estimat…
updated 6.9 years ago • Nicola
Hi,
I m having error in installing DESeq2 on my mac.
library(DESeq2)
Error: package ‘RcppArmadillo’ required by ‘DESeq2’ could not be found
sessionInfo
updated 8.2 years ago • seeker
I would like to convert R codes R codes in /DESeq2/R/ to HTML, but after conversion \\code{\\link{...}} are ignored. Would you please let me know I can convert them properly
updated 8.7 years ago • mariamari693693
I used DESeq2 to do my Differential gene expression analysis for my RNA seq data. I would like to know what script I can use to generate
updated 5.2 years ago • adeler001
Hi,
Apologies, this might sound like a very basic and already asked question. I am new to DESEQ2 and have a naive question regarding the analyses of a 2 x 2 factorial design and result interpretation.
First, I am interested
updated 10 months ago • Len
Hi,
I'm using the function RUVg in the RUVSeq package to analyse my RNA-seq data and then to DEseq2. I have 50 samples. Im following the steps of Love et al. where as factor k they propose k=1 (https://bioconductor.org/packages...packages/release/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html#using-ruv-with-deseq2) they use k=2.
The problem is i dont know whick k to use and what is do…
updated 19 months ago • Ειρήνη
Hi there, I am perfoming DE between different age groups, working on lncRNAs as well as mRNAs. As an initial step, I separated my countdata for lncRNAs and performed DE using DESeq2. From my understanding is that alpha argument should be set to the same FDR that is going to be used so I set it to 0.05
```r
contrast1 <- c("AGE", "30_39yrs" , "20_29yrs" )
res_l_2to1 <- results(dsl, c…
updated 3.3 years ago • a.khazaal
Since I'm analyzing my SLAM-seq data for the first time, I thought I'd follow this guide: https://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html...Since I'm analyzing my SLAM-seq data for the first time, I thought I'd follow this guide: https://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#quick-start
In the guide, it says to use contras…
Hi,
I've been playing with Deseq2 to normalize and analyze my datasets, initially only out of curiosity. The results look more reasonably to me than...Hi,
I've been playing with Deseq2 to normalize and analyze my datasets, initially only out of curiosity. The results look more reasonably to me than results...or genome equivalents). However, it is unclear to me if you would actually encourag…
updated 6.1 years ago • zoraurora
like to get feedback about model designs and contrast dealing the issue of "Model not full rank" in DESeq2.
The sample meta info:
```r
library(magrittr)
s_meta <- data.frame(grp = paste(rep(c("D", "L", "M", "H"), times = 2), rep(c("6h", "24h"), each = 4), sep = "_") %>%
rep...times = 12) %>%
factor(levels = c("D_6h", "L_6h", "M_6h",…
updated 22 months ago • ccshao
Hello, I am new in DEseq2 analysis. I have tried to analyze my RNAseq data with GSEA software from Broad institute but didn't find anything satisfactory...I came across DEseq2 as most of the researchers use this approach. I will try to briefly explain my data that might help understand if there
updated 5.9 years ago • golam.mohiuddin
Hi Michael, I am following up on our previous discussion, I ran DESeq2 with `` minReplicatesForReplace=Inf `` and `` cooksCutoff=FALSE `` and it actually increased the number of DE genes. ...cooksCutoff = FALSE);</pre>
<span style="line-height:1.6">The big difference between deseq and deseq2 is there thousands of DE genes, even with 0.01 FDR. Is there any other crite…
updated 11.0 years ago • Prasad Siddavatam
who would like to know if I am designing my differential expression experiment correctly using DESeq2. I performed RNA-seq on tissues originating from 14 total animals at 4 time points of exposure to a drug. 3 animals were...Ac11 BG 1hr
I want to make several multifactor comparisons.
1. First, I would like to compare a time course of the drug effects (treatment) on eac…
updated 8.4 years ago • Caleb Bostwick
div class="preformatted">Hi, All,
In UCSC and BioMart is there some transcription factor binding site
data base I can use for bioinfor analysis for some genes in Drosophila
or other species?
all best
Zhi Zhang
updated 14.0 years ago • Zhi Zhang
When I load the DESeq2 package, this error shown in the attached image below occurs. Can anyone help me with it? I would really appreciate any...help! Thank you!**
![enter image description here][1]
**I am able to find the DESeq2 file in the local path, but it's unable to be loaded. The following image shows the sessionInfo() information:**
![enter image
updated 2.9 years ago • joanna
For downstream analysis using a modified version of Robust Rank Aggregation (alpha-RRA; Li, et al. Genome Biology 2014), I would like to obtain __one-tailed p-values__ from a standard DESeq2 analysis using a Wald test (rather than the two-tailed p-values that are represented in a 'DESeqResults' object). Can...nbsp;Li, et al. Genome Biology 2014), I would like to obtain __one-tai…
updated 7.3 years ago • t.kuilman
I can't dowload DESeq2 onto my laptop, although it was no problem on the desktop computer sitting right next to it. Here is the end of the installation...LC\_MONETARY failed, using "C"
ERROR: dependency 'genefilter' is not available for package 'DESeq2'
\* removing '/Library/Frameworks/R.framework/Versions/3.2/Resources/library/DESeq2'
The downloaded source packages...status
2…
updated 9.0 years ago • cclayton
I downloaded R 4.1.2 64bit and downloaded DESeq2 in R by
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("DESeq2")
Install information...packages/release/bioc/html/DESeq2.html
My code DESeqDataSetFromMatrix use to work in R-3.1.2. with DESeq2 downloded from biocLite.
Now with newer version R and DESeq2, I got the following error. Could anyone h…
updated 3.9 years ago • pam
Hi,
I am trying to use DESeq2 to convert raw counts to fpkm, so I can compare gene aboundance across genes and not only across samples. I have a couple...of questions on how to do so:
1. Should I first normalize the counts and transform them with vst and then use the `` fpkm() `` function, or should I simply input the raw
updated 6.8 years ago • chiara.facciotto
assembled a transcriptome de novo, and now wish to carry out differential expression analysis using DESeq2. The RIN varies between samples for a variety of reasons, and by the nature of our study system we could not simply refine...dds)
![enter image description here][1]
vsd <- vst(dds, blind=FALSE)
Group <- factor(colData(vsd)$Group)
RIN <- samples$RIN…
Hello,
I have a question about analysis using DESeq2.
I have three samples of different time points without replicates.
I want to check the genes whose expression level...to analyze using these continuous variables?
Or Is there any commendable method of analysis using DESeq2?
Thank you in advance
updated 6.7 years ago • snu_jh
following the standard RNA-seq analysis workflow to make sense of some experimental data, using the DESeq2 package. Here is the MA-plot I have:
I am not concerned about the low log-fold change
updated 7.8 years ago • ap_vc21
Hi all,
I have a data set with both paired samples and confounding factors. I want to use limma to find the differential expressed genes, but I don't know how can I design the design matrix. Could...Hi all,
I have a data set with both paired samples and confounding factors. I want to use limma to find the differential expressed genes, but I don't know how can I design the design matrix. Could a…
updated 7.2 years ago • yuabrahamliu
a "reasonable" proportion?
Can I make it a little less stringent in some way?
Note that I was first filtering with `dmFilter()`, which I then removed to see if that made a difference, but it doesn't.
On this data set I first performed...the differential expression analysis at the gene-level using DESeq2, and then was asked to perform the differential transcript usage, so I gave DRIMSeq a…
div class="preformatted">Hi Mike,
I am using DESeq2 package for my project now, and I have some
questions
regarding to this pacakge.
Please let me briefly introduce some...background information about my
project. I have three factors: A with 16 levels, B with 2 levels and C
with
3 levels, in total 16*2*3=96 groups. There are 8 biosamples for each
group,
hence...up 726 biosamples, hence it is…
Looking to reallocate more application memory to DESeq2 because when running:
betaPrior = TRUE
On a large matrix, I run out of application memory. Anyone have ideas how to get...Looking to reallocate more application memory to DESeq2 because when running:
betaPrior = TRUE
On a large matrix, I run out of application memory. Anyone have ideas how to get around
updated 7.2 years ago • rbronste
In DESeq (1, as it were) there's a way to "turn off" dispersion. Can this be done in DESeq2 as well? Might be helpful when sample sizes are large (I have a data set with 66 samples) and dispersion may mask some "real
updated 9.9 years ago • hans
I am using deseq2 to find differential significant taxa (count data). The data is longitudinal and three groups of mice and I am using...nbsp; team + condition:week_experiment)</code>
since I have three groups, I wonder how DEseq2 is calculating the fold change and p-value !? There is neither any warning nor any error ! should I slice the data 3 different
updated 9.3 years ago • akp
Hello,
I have RNA-seq data that I would like to visualize via a GOterm heat map between time points. I have successfully been able to run DESeq2 on my transcriptome, but the output file with logpvalue/pvalue is my entire transcriptome, not compartmentalized by time point (0, 6, 12, 24, 48hr). I was able to make a heat map from this via time point but again, I have A LOT of genes so wanted to gro…
A gene in my dataset has average counts of 0 (control) vs. 13.3 (treated). My DESeq2 analysis determines the gene to have a padj = 5.8E-6 and an average LFC of 6.6.
1) How can a LFC value be calculated in this...test could potentially yield padj ≤ 0.05, this isn't a hit I would follow up on. Anyone have first-hand experience or know of literature that determines whether such small shifts in…
updated 4.9 years ago • vanbelj
raw_counts,"C:\\Users\\USER\\Desktop\\countsdata.csv")
#load library
library(DESeq2)
#/ make a DESeq2 object. We can parse the group membership (Mild etc) from the colnames,
#/ which are based on the original filenames...dds <- DESeqDataSetFromMatrix(
countData=raw_counts,
colData=data.frame(group=factor(unlist(lapply(strsplit(colnames(raw_coun…
Bioconductor support community,
I have ribosome profiling/RNA-seq data that I want to analyze using DESeq2, but I am having some trouble with the design and how to compare selected samples. I'd really appreciate your help!
I have
updated 7.4 years ago • kotcha.m
the number of SVs, only used 2.
My question is: should I go with 2 or 9 for the subsequent DESeq2 analysis here?
Thanks for any inputs!
C
What is the best way to extract the expression matrix, once deseq2 has undertaken it's analysis, if I want to analyse the pre-deseq2 against the post-deseq2 expression matrix using PCA
updated 14 months ago • agamemnon
div class="preformatted">Hi Simon,
2 questions:
(1)
I am working with a multi-factor experiment that, in a sense, doesn't
have biological replicates (replicates were done at different times,
and
the differences...2)nd question:
Also, a followup question (I've since done the pairwise comparisons w/
the mult-factor design); is there a 'baseMean' stored anywhere within
the multi-factor experime…
updated 13.7 years ago • Ingrid Lindquist
I am having trouble installing DESeq2:
biocLite("DESeq2")
BioC\_mirror: https://bioconductor.org
Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2...var/folders/bt/j1th0gjn1mbdgcr1xh1x3bgw0000gn/T//RtmpmPeLAW/downloaded\_packages
> library("DESeq2", lib.loc="/Library/Frameworks/R.framework/Versions/3.3/Resources/library")
__Loading required package: S4Vectors..…
updated 8.5 years ago • nidz91
that I run:
```r
##CREATE THE METADATA FILE##
sample_names <- colnames(cts)
condition <- factor(rep(c(rep("Control",12), rep("Treated", 12)), 2), levels = c("Control", "Treated"))
Replicate <- factor(c(rep(1:3, 4), rep(4:6, 4), rep(7:9, 4), rep(10:12, 4)), levels...c(1,2,3,4,5,6,7,8,9,10,11,12))
Sequencing_run <- factor(c(rep("A", 24), rep("B",24)), levels=c(…
updated 3.2 years ago • Flavio
Hi,
I am reading through the DESeq2 manual and saw the different examples in the results help page. I have a couple of questions to make sure I am understanding...Hi,
I am reading through the DESeq2 manual and saw the different examples in the results help page. I have a couple of questions to make sure I am understanding these things properly. I am focused more on "Example 3: two conditions, t…
updated 10.6 years ago • Aggarwal, Praful
Hi,
I've got an error in a DESeq2 analysis by running code:-
dds <- DESeqDataSetFromMatrix(countData = countData, colData = coldata, design = ~ Conditions...in the model matrix.
Please read the vignette section 'Model matrix not full rank':
vignette('DESeq2')
In addition: Warning message:
In DESeqDataSet(se, design = design, ignoreRank) :
some variables in design formula are chara…
paired reads mapped to the fasta file
Then, the corresponding h5 abundance files were imported into DESeq2 using tximport, and a DE analysis was performed. That was pretty easy as only two conditions were compared
I was certainly...Change over 256. This change could be very meaningful for me from a biological point of view.
My first expectation is that the t3 isoform should have some component…
hi
I want to analyze the TCGA data with the DESeq2 package.
As you know there are three types of data in this database.
This site (http://seqanswers.com/forums/showthread.php...t=42911) provides information on these three types of data.
1- raw counts:
The (first) RSEM paper explains that the program calculates two values. One represent the (estimated) number of reads that aligned
updated 5.7 years ago • roohallah1435
Recent ...
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