Questions tagged [deseq2]
The deseq2 tag has no usage guidance.
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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 , ...
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2answers
77 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
50 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,...
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1answer
69 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 ...
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1answer
20 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 ...
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1answer
54 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
21 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
39 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 ...
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77 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 ...
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1answer
63 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
45 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
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1answer
37 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 ...
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2answers
210 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
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1answer
96 views
Removing genes with less than a correlation cut-off between two matrices
I have two matrices like this:
...
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57 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
64 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
61 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
459 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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2answers
303 views
DESeqDataSetFromTximport invalid rownames length
I am trying to use DESeqDataSetFromTximport function from DESeq2 package to construct dds ...
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2answers
145 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
338 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
66 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.
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1answer
200 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
173 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
131 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
677 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
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
224 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
564 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
58 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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1answer
38 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
494 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
77 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
44 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
272 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
87 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
75 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
413 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
228 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
106 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
98 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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2answers
371 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
341 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
313 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 ...
7
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1answer
553 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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2answers
506 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 ...
5
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1answer
468 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 ...
10
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2answers
378 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
3k 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 ...
