Questions tagged [deseq2]

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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

Comparing factor levels in deseq2

I have sample information (sampleinfo) in this format: ...
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
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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
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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
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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
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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. ...
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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
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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
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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
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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. ...
3
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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
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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
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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
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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
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2answers
412 views

DESeqDataSetFromTximport invalid rownames length

I am trying to use DESeqDataSetFromTximport function from DESeq2 package to construct dds ...
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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
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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
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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
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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
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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
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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
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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
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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 ...
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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 ...