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Questions tagged [deseq2]

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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 ...
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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 ...
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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 ...
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1answer
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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 ...
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2answers
108 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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1answer
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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 ...
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1answer
62 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 ...
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1answer
53 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: ...
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3answers
277 views

Install DESeq2 through anaconda

I tried running conda install -c bioconda bioconductor-deseq2 in a conda environment, but when I run ...
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187 views

DESeqDataSetFromTximport invalid rownames length

I am trying to use DESeqDataSetFromTximport function from DESeq2 package to construct dds ...
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2answers
66 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 ...
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1answer
218 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 ...
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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. ...
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1answer
142 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 ...
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1answer
75 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 ...
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3answers
114 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 ...
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2answers
421 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: ...
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2answers
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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
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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 ...
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1answer
372 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 ...
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1answer
51 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?
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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 ...
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1answer
329 views

Highly variable genes analysis by DESeq2

In the following article. There are two ways of getting highly variable genes: ...
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1answer
69 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 ...
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1answer
41 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 ...
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1answer
206 views

Salmon tximport

I ran bulk RNA-seq experiment and got quant.sf file. Now, I am struggling with understanding what ...
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1answer
74 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 ...
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1answer
70 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 $j$...
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1answer
190 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 ...
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1answer
152 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?
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1answer
91 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 ...
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1answer
86 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 ...
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294 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 ...
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2answers
288 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 ...
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2answers
274 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 ...
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1answer
433 views

Trouble using biomaRt to retrieve hgnc symbols from Ensembl transcript ids

I have a matrix of gene counts which I'm going to use as input for DESeq. Right now, each gene is labeled by its Ensemble transcript ID, but I'd like to convert these to their HGNC symbols before I ...
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414 views

Running differential expression analyses on count matrices with many zeroes

Note: I also posted this issue (with less context) in the bioconductor support site: https://support.bioconductor.org/p/97424/ I'm working on a snakemake workflow that identifies various small RNA ...
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1answer
389 views

What are the ways to process a list of differentially expressed genes?

We are studying six different human macrophage/dendritic cell types isolated from healthy skin. They all differ from each other in a few cell surface markers. We are interested in the characteristics ...
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2answers
312 views

Can I model technical replicates in DESeq2?

I’d normally use collapseReplicates (or do the collapsing upstream) to handle technical replicates. However, in my current RNA-seq experimental design, samples ...
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2answers
1k views

How can I extract normalized read count values from DESeq2 results?

The results obtained by running the results command from DESeq2 contain a "baseMean" column, which I assume is the mean across samples of the normalized counts for ...
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2answers
2k views

Understanding DESeq2 design, contrast and results

I have a set of high-troughput experiments with 2 genotypes ("WT" and "prg1") and 3 treatments ("RT", "HS30" and "HS30RT120"), and there are 2 replicates for each of the genotype x treatment ...