Questions tagged [deseq2]
Deseq2 is an R package for analyzing RNA sequencing data
64
questions
3
votes
1answer
47 views
How to design DESeq2 LRT model with individuals nested in 2 levels?
We have a complicated experimental design that we would like to perform LRT analysis for. Our main goal is to discover significant genes for the "Injection:Social" interaction term across ...
0
votes
1answer
50 views
DESeqDataSetFromTximport all(lengths > 0) is not TRUE
I am suddenly running into an error when running the DESeqDataSetFromTximport
...
1
vote
1answer
25 views
Is it conflicting: significant difference according to Wald test but not in PERMANOVA and ANOSIM to compare species abundances of metagenomic samples?
If there is no significant difference between two groups of metagenomic samples according to "Multivariate differential abundance tests" for example PERMANOVA and ANOSIM, does it makes sense to use "...
0
votes
2answers
35 views
Ranking metric in GSEA
I am using fgsea in r to calculate and plot a bunch of GSEA graphs.
My question is whether it is acceptable to use the Wald statistic from DeSeq2 to rank the gene list?
I have seen in the GSEA ...
0
votes
1answer
38 views
How to incorportate RIN values as covariate in the design matrix?
I have been following the last DESeq2 pipeline to perform an RNAseq analysis with a dataset with low rin samples in the experimental (or treated) and high rin on the control ones.
I read a paper in ...
2
votes
1answer
52 views
Should biological replicates be the most similar pairs in an RNAseq experiment?
The attached figure (from deseq2) shows the sample to sample distances of a RNAseq experiment with 4 conditions (A,B,C,D) at 2 time points (0h,4h) with 2 biological replicates.
I am a little bit ...
1
vote
2answers
32 views
Identify differentially covered genes only between two samples
I have a question about finding differentially covered regions (coverage represents methylation level which goes from 0 to several thousands). I'm using enrichment based method which can be summarized ...
2
votes
0answers
29 views
vst() from DESeq2 vs voom() from limma
I have used both to transform my leukaemia RNA-Seq data for subsequent hierarchical clustering. The result is quite different. Some subtypes of leukaemia only form a cluster (or at least sit closer) ...
1
vote
1answer
25 views
DESeq2 compare within a condition
This might be a really stupid question, but I can't figure out how to do this. I've read through the DESeq2 vignette and manual pages but couldn't find an answer.
I have a bunch of samples split up ...
2
votes
2answers
30 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
vote
1answer
57 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
votes
1answer
46 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
votes
2answers
494 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
27 views
0
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1answer
80 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
85 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
votes
2answers
173 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
91 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
126 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
46 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
votes
1answer
68 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
votes
1answer
144 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
vote
0answers
221 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
89 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
166 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
votes
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
767 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
166 views
Removing genes with less than a correlation cut-off between two matrices
I have two matrices like this:
...
0
votes
0answers
59 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
69 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
2answers
197 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
3answers
1k 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
495 views
DESeqDataSetFromTximport invalid rownames length
I am trying to use DESeqDataSetFromTximport function from DESeq2 package to construct dds ...
1
vote
2answers
339 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
620 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
259 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
278 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
466 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
180 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
1k 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
428 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
1k 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
72 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
votes
1answer
43 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
votes
1answer
944 views
Highly variable genes analysis by DESeq2
In the following article. There are two ways of getting highly variable genes:
...
4
votes
1answer
94 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
votes
1answer
46 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
348 views
Salmon tximport
I ran bulk RNA-seq experiment and got quant.sf file. Now, I am struggling with understanding what ...
4
votes
1answer
99 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 ...
