Questions tagged [deseq2]
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56
questions
2
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2answers
29 views
Is there a computational tool or possibility to identify mRNA isoforms from the count matrix of a bulk RNA sequencing dataset?
I have the counts matrix of an RNA sequencing dataset of fibroblasts and I wish to identify isoforms of a particular gene of interest in it. Can anyone please hint me on a bioinformatics method to ...
1
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1answer
33 views
How do I differentiate outliers from in-group variations in a DESeq2 PCA plot of 9 samples distributed into 3 conditions?
I have a PCA plot from DESeq2's plotPCA(vsd, intgroup=c("conditions")) function. I have 9 samples distributed in to 3 groups of 3 biological replicates each. My ...
-2
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1answer
42 views
How are these definitions related to differential expression?
I have two groups of patients; for each patient I have an output file (RNA-seq) contains this information
...
2
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2answers
117 views
STAR quantMode vs RSEM vs Kallisto
I recently discovered this Snakemake pipeline for RNASeq that uses STAR's quantMode to quantify gene expression for DESeq2 differential expression analysis.
In the past I've always seen the workflow ...
0
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1answer
25 views
0
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1answer
53 views
RNASeq: Normalization, stabilization, gene length and rlog
I was thinking about the best method for normalization, which takes gene length into account (in order to compare genes)...
Do you think I can do that? :
- taking raw counts and dividing each gene by ...
0
votes
1answer
84 views
How I deal with this kind of gene expression comparision
I have RNA-seq from two sequencing batches; Lab technician says that he has run the RNA expression quantification two times in bathes 1 and 2 for example tumor 1 in batch 1 and tumor 1 in batch 2 , ...
0
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2answers
109 views
Interpreting this PCA plot for RNA-seq
I have RNA-seq from two sequencing batches; Lab technician says that he has run the RNA expression quantification two times in bathes 1 and 2 for example ...
1
vote
1answer
78 views
Comparing RNA-Seq and Ribo-Seq
I'm attempting to compare total RNA-seq with Ribo-Seq, to determine if changes in Ribo-Seq are due to changes in transcriptional expression (akin to the analysis performed by Anota2Seq). I am, however,...
0
votes
1answer
105 views
Correlate DEGs from DESeq2, EdgeR and Limma results
I have a lists of DEGs identified by DESeq2, EdgeR and Limma.
I would like to correlate the the gene rankings in the lists to decide on a package to use in downstream analysis.
I am havig a few ...
0
votes
1answer
38 views
Single sample in group: normal pipeline or Kal's Z test
As stated, which one is better for differential expression analysis? When I say normal pipeline I mean limma-voom, edgeR and DESeq2 pipeline for standard analysis. Kal's z test is mentioned in this ...
5
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1answer
57 views
design formula question
I am not sure I am building the proper design formula for the question I want to answer
I have the following samples with three factors; clone, the structure and the condition.
...
0
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0answers
42 views
Normalization for microbiome 16s sequence analysis
The way I understand things, normalization (such as in DeSeq2, EdgeR, etc.) serves two purposes: 1) Model the "real" abundance in the original samples from the read counts, 2) Make the abundance ...
0
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1answer
66 views
Why does DESeq2 convert numeric columns to factor during differential expression analysis?
I'm attempting to perform differential expression analysis using DESeq2 on a dataset of ~90 samples and ~20000 transcripts. I have a number of variables I'd like to test against, some of which are ...
1
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0answers
160 views
Is it advisable to remove X and Y chromosome genes in a bulk RNA-seq dataset at the level of the count matrix?
From this link remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline, I have learned that depending on context, it is perfectly valid to remove X and Y chromosomal genes in an RNA-seq ...
2
votes
1answer
85 views
How to get log2 fold change of RNA-Seq data for time series experiment?
I know if there is one control and one treatment group it is pretty straight forward to interpret log 2 fold change. But, I have time course experiment. I have infected cells with viruses and I ...
0
votes
1answer
100 views
Differential expression analysis when nested effects
I have 3 tumour samples from 3 patients from an experiment, I also downloaded 10 normal samples from TCGA. My design is like this
...
-1
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1answer
38 views
Finding genes especific to microenvironment
I have RNA-seq .bam files for 3 patients, tumour and its matched derived model, namely organoid, but I don't have any matched normal sample.
Differentially expressed genes between a tumour and its ...
3
votes
2answers
441 views
Installing DESeq2 in Ubuntu
I am trying to install DESeq2 in my Ubuntu with R version 3.5.1. According to the package repository in Bioconductor the version should be 3.5.
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3
votes
1answer
135 views
Removing genes with less than a correlation cut-off between two matrices
I have two matrices like this:
...
0
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0answers
58 views
Making a model of gene contribution in cancer diagnosis
I have raw read counts (Edgeseq technology) of 56 patients who have been ranked with Mandard score as responders and non-responders;
I have done differential expression by DESeq2 and I obtained a ...
0
votes
1answer
65 views
Experimental Design for Differential expreression analysis
I have a Normal esophageal Fibroblasts (NOFs) cultured in DMEM media; The same NOF also have been cultured with a tumor sample from a patient named 005 on DMEM media; I have also Cancer Associated ...
3
votes
1answer
87 views
PCA plot shows big difference but not many differentially expressed genes are found
I got a PCA plot of bulk RNA-seq experiment that looks the following way:
It was generated by the following code:
...
2
votes
4answers
763 views
Install DESeq2 through anaconda
I tried running conda install -c bioconda bioconductor-deseq2 in a conda environment, but when I run ...
3
votes
2answers
412 views
DESeqDataSetFromTximport invalid rownames length
I am trying to use DESeqDataSetFromTximport function from DESeq2 package to construct dds ...
1
vote
2answers
272 views
levels of factors in the design have non-unique level names after make.names() is applied
When I try to import the data using DESeq2 package:
dds <- DESeqDataSetFromTximport(txi, sampleTable, ~Group + Cre)
I am ...
2
votes
1answer
504 views
How to get the corrected matrix after SVA batch effect correction
I ran SVA to remove batch effects for my bulk RNAseq experiments, but now I need to somehow correct my data matrix in order to ...
2
votes
1answer
176 views
How to input data for DESeq2 from individual HTSeq count?
I am comparing the gene expression of 2 bacteria under 1 condition. I have now the count tables for 3 tech. replicates for each bacteria.
...
1
vote
1answer
247 views
Compare clusters from different datasets
I have two scRNAseq datasets, and I select a cluster from one of them, and another cluster from the other. I want to find differentially expressed genes between the ...
1
vote
1answer
308 views
DESeq2 complicated design - effect of replicated samples
I have RNAseq data from a relatively complicated experimental design with variables = genotype, treatment, time, and batch. I have 2 biological replicates for each genotype/condition, however ...
2
votes
3answers
160 views
Selection of differential expressed genes
I'm working with RNA-seq data. I have 40 tumor samples and 5 Normal samples. Differential analysis with Deseq2 based on Fold change > 1.2 and alpha < 0.05 gave ...
3
votes
2answers
987 views
gene-level versus transcript-level analysis
Traditionally, RNA-seq data was quantified on gene level. Newer methods quantify on transcript/isoform level. For example, Kallisto only outputs transcript-level abundances. From the DESeq2 vignette:
...
2
votes
2answers
39 views
Can I ask DESeq2 which variable alone explains which gene's behavior the best?
Imagine I have a dataset of highly periodic gene expression, taken at densely spaced timepoints. I know that the expression is periodic, but different genes have different offsets.
It is trivial to ...
1
vote
0answers
290 views
Likelihood Ratio Test in DEseq2
I have a RNA seq data which I am trying to identify DEGs. Dataset contains:
Untreated - 2 replicates (time point 1st day)
Treated - 4 replicates (2 replicates at 3rd day & 2 replicates at 7th ...
0
votes
1answer
843 views
Transform and feed data into DESeq2 with DESeqDataSetFromMatrix
There is a normalized expression matrix. I split it into two and want to do DE on the two cells' subsets. I am having trouble ...
0
votes
1answer
68 views
differentially expressed intron analysis?
I have used Deseq for estimating the differentially expressed introns for the RNA seq data using the UCSC intron bed file. can Deseq be used for differentially expressed intron analysis?
0
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1answer
41 views
Deseq2 output issue
3 Control replicate and 2 test sample ,so Im comparing my Control which is my Progenitor cells to Monocyte which is mature stage
this is my code im using
...
0
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1answer
749 views
Highly variable genes analysis by DESeq2
In the following article. There are two ways of getting highly variable genes:
...
4
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1answer
92 views
plotMA function issue: can not circle genes
I am trying to make MA-plot for my bulk-RNA-seq dataset and experiencing issues with it. I just copy-pasted the code that can be ...
0
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1answer
45 views
DeSeqDataSet experimental design: column with integer values
I am creating DeSeqDataSet and I am unsure whether I need to include the number of mice into the design formula. Basically, the samples look like that:
I have 4 ...
2
votes
1answer
322 views
Salmon tximport
I ran bulk RNA-seq experiment and got quant.sf file. Now, I am struggling with understanding what ...
4
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1answer
93 views
LRT or LRT-like test on cyclical (Sleep) data
I have RNA-Seq data from 4 time points (3 hours awake, 9 hours awake, 3 hours asleep, 9 hours asleep). I'm interested in doing something similar to a LRT where genes are found to be significant if ...
1
vote
1answer
81 views
Negative binomial modeling of RNA-Seq data
A common way to model RNA-seq data is using a negative binomial distribution, where each sample-gene pair is modeled by a different negative binomial distribution with mean $\mu_{ij}$ where $i$ and $j$...
2
votes
1answer
684 views
Error in checkFullRank(modelMatrix) deseq2
Trying to use deseq2 for differential expression analysis (rna-seq) between three groups and also account for batch effect as the control were sequenced at a different time point.
control: con
...
5
votes
1answer
278 views
What are the count units in DEseq2?
This is a pretty silly/simple question, I suppose.
What units are DESeq2 counts? Or are the units arbitrary but internally consistent estimate of actual reads?
2
votes
1answer
142 views
Why do I obtain very strange results with DESeq2?
I am using DESeq2 to perform a differential expression analysis, but I obtained very strange results for some genes. For some genes, I have very high log2FoldChange with very low p-value as displayed ...
5
votes
1answer
129 views
How can I specify to DEseq2 to only perform comparisons on which I am interested with?
I am currently performing a large RNA-seq analysis from mice PBMCs. The dataset contains around 6,000 transcriptomic profiles and I would like to use DESeq2 to identify the sets of differentially ...
10
votes
2answers
493 views
*very* unbalanced group sizes for DE
I downloaded some publicly available RNA-seq data and want to compare those samples carrying a mutation (~4) against the rest (~800!). I ran both EdgeR and DESeq2, and the first results in an ...
5
votes
2answers
397 views
Is it possible to create a DESeqDataSet with a user-provided design matrix?
I'm trying to run a differential gene expression analysis using DESeq2, with counts coming from kallisto. I have imported them using tximport and I'm creating the ...
7
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2answers
367 views
differential gene expression complex design no replicates
We have an experimental design as seen below
Where we administered drug at 0 min for each mouse genotype and took them down at given below intervals. wt and ko mouse models were administered only ...
