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Questions tagged [deseq2]

Deseq2 is an R package for analyzing RNA sequencing data

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Is it normal to have low mapping to bacterial genome in a total RNA sample of plant root-colonized bacterial cells?

I had isolated the total RNA from a sample of plant roots with colonized bacteria by excising the roots (harboring the bacterial cells) and crushing them into a powder using liquid nitrogen. The RNA ...
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rna seq matrix design hybrids

I am struggling to get my head around the correct design to use for my experiment. I have RNAseq of 2 pure species (s1, s2) and of the hybrid (h). I aligned all three genotypes to the s1 genomes. I am ...
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Multi Factor in Deseq2 Gene enrichment analysis

I want to see how the gene expression differs in breast cancer between three species, and I am using DESeqDataSetFromMatrix on my count table. ...
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Continuous predictor variable to identify responder genes using DESeq2

I have samples from 45 individuals at 2 time points and these individuals were given a specific diet. The BMI of these individuals were recorded at both time points. The responders to the diet are the ...
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How to incorporate negative controls in DESeq2

We are doing a comparison between two outcomes (positive and negative). We could not have any positive controls as we do not have any "control" data to set as baseline, either from ...
Karthik Nair's user avatar
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how is log2foldchange calculated in DESeq2

I am trying to calculate log2FoldChange in DESeq2 by hand because I am trying to reproduce my results and understand how DESeq2 works. What I want to know is: Are the counts first fitted to a ...
Guri Giaever's user avatar
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enrichment of DE genes within wide regions not pathways, hypergeometric test or GSEA?

I haven't found any relevant posts, so here is my question (it's more a question on statistics I believe): I have the deseq2 output of DE genes( around 25000 genes) , and among them 1000 are ...
dew's user avatar
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Understanding DESeq2 output for resultNames

I'm following along with some pre written code to learn how to do differential expression. I am using the same data set and have gone back through the code and copy and pasted what they used and the ...
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Issue with Differential Gene expression analysis with Deseq2

I am using the Deseq2 package to perform a DE analysis on multiple factors. So, basically to perform the analysis I consider patients characterized by the Brugada Syndrome type 1 and other patients ...
Alessia Avon's user avatar
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Correlation heatmap of RNA-seq clusters all samples together leading to very low no. of DEGs

I am writing to you to take an input or may be you can provide a different perspective. I am at wits end :( So I have nearly 200 samples. These are separated into two groups (group I treated with ...
Angelo's user avatar
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Integrate bulk RNA and ATAC-seq genes

I have up and down-regulated genes from bulk RNA result from DeSeq2. Genes that are differential in chromatin accessibility between two conditions from DiffBind. I would like to find the genes overlap ...
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DESeq2 throwing error while normalizing raw microarray expression data due to presence of negative values

This question was also asked on Biostars I am trying to download and analyze a miRNA expression dataset from NCBI GEO (GSE25631). I specifically want non-normalized ...
accibio's user avatar
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RNAseq alignment: best practices for aligning to multiple isoforms?

I have Illumina RNAseq data and would like to maximize my power to find candidate genes that are differentially expressed genes between experimental conditions. Many of my (de novo assembled and ...
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Differential gene expression: how do I correctly compare three groups to each other?

I'm trying to figure out the right way to do differential gene expression analysis with a discrete variable with three groups. The context is, I want to assess differential expression as a function of ...
mrz123456's user avatar
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Batch correction in differential expression analysis

I have sent two sets (two batches in matter of sending for sequencing) of different samples (plasma) to small RNA-seq to Qiagen company This is how my meta data look ...
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Manually calculating log2 fold change values from DESeq2 normalized counts [closed]

This question was also asked on Biostars and Bioconductor Support My aim is to perform gene clustering based on RNA seq datasets (raw expression values) from NCBI database. After clustering I realized ...
jayesh kumar's user avatar
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DESeq2 for large number of samples takes too much RAM

I am trying to run a very large number of transposase-accessible chromatin (ATAC)-seq samples through DESeq2 to find peaks of differential chromatin accessible across my study genome. I have about 100 ...
Shashank Nagaraja's user avatar
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DESeq2 and EdgeR

I am new to using both DESeq2 and EdgeR in Bioconductor used for transforming my RNA expression data. However, I am struggling to understand their specific purpose, differences between them and ...
noor fatimah's user avatar
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Filtering reads greater than 5 from HT-seq count files

I have some raw counts from HTSeq after aligning with hg38 human reference genome. I want to do filtering in a way that the filtered count files should have the same number of lines. The reason behind ...
Aranyak Goswami's user avatar
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Creating multiple phenotype datasets using bootstrap method "Bootstrap-samples-by-column-of-a-data-frame-in-r" for DEG analysis

I am working on a datasets and after some discussion with my group, we doubt that maybe one or more of our controls are different than the other controls. The motivation is to see if one or more ...
salman1490's user avatar
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4 answers
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nested samples in design DEseq2

I'm running a DEG analysis with Deseq2 by specifing the following design that includes 12 samples from 6 pts in 4 different conditions: ...
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Basic RNA Differential Expression in R

I have two matrices, one for individuals before treatment and one for the same individuals after treatment. Both matrices are raw read counts of RNA expression. ...
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deseq2 single factor design output interpretation

This is regarding the single factor design For example if I have Age or other continuous numerical variable how to provide that into the design formula. For this post do i need to 'You could ...
kcm's user avatar
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deseq2 model design : Different gene output

Here I have two designs: Design 1 ...
kcm's user avatar
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deseq2 makeContrasts function

This article talked about various deseq2 designs etc. One of the designs I would like to use is explained as this: Control versus treatment average ...
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deseq2 full and reduced model interpretation

I would like to know how to interpret the output of the formula although i been thorough loads of literature but I'm not confident yet. So this is my full model I'm running ...
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Different results of DESeq2 in different ways of comparison

I have different treatments (infected and control ones). When using DESeq2, I have different results in two ways of comparison. first way: factor: treatment, factor level1: Moribund Infected, factor ...
Zohreh's user avatar
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604 views

What is the difference between Normalized Expression in EdgeR vs DESeq2?

I am trying to access the normalized expression in both edgeR and DESeq2, yet the results are different. Does anyone know why? How to get normalized expression using edgeR: ...
Nova's user avatar
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baseMean threshold

I have an RNA-seq dataset and I am using DEseq2 to find differentially expressed genes between the two groups. I used pre-filtering to remove any genes that have ...
suzie321's user avatar
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1 answer
150 views

Error in DESeq2 analysis with dimnames

I'm getting the following error in a DESeq2 analysis and I can't seem to figure out the issue: ...
Nova's user avatar
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LRT test in deseq2 on multiple condition

I have some doubts when i'm running LRT This is my condition data-frame small subset ...
kcm's user avatar
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522 views

How to input data and metadata from NCBI for RNA-Seq analysis in R

So, I have downloaded some .txt and .csv files containing the raw count data (I am supposed to find out differentially expressed genes and see which genes and up- and down-regulated). I have also ...
Addy's user avatar
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How does DESeq2 "collapseReplicates()" function work on read counts data?

Comparing read counts from an RNA-seq experiment for two select genes before and after using DESeq2's collapseReplicates() and ...
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Batch Effects that are Close to Collinear with Main Effect

Two years ago, I started working on a project uses both RNAseq and ATACseq. It's supposed to be a simple Healthy Control (HC) vs disease study. The sample collection was done in 2 phases, and it was ...
Jeff's user avatar
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How to remedy a DESeq2 collapsing technical replicates error?

Goal: To ensure "the sum of the counts for [my samples] is the same as the counts in the [samples] columns in ddsColl" after collapsing replicates using ...
Gawain's user avatar
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Use of "baseMean" in DeSEQ2

The basemean is described as the "mean of normalized counts of all samples". My question is, how would we interpret differences in basemean between genes, pertaining to reliability and such? ...
CodeMonke's user avatar
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Visualizing top expressed genes

I have a spreadsheet of CPM values I want to visualize the top 20 genes expressed across my samples This is how my data look like ...
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Best R program to use for RNA seq analysis

We have an RNA seq taken from a the same tissue in two different developmental stages. We have one gene, with the number of reads from stage A and stage B, and we want to see which genes are ...
Merav Gold's user avatar
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49 views

The correct design for time series experiment

I have a treatment and control in two time points like this ...
Zizogolu's user avatar
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How to simulate replicates for DGE analysis?

I am prototyping with data visualization of DGE results, and I would like to work on the analysis pipeline before the real data is available. Currently, I only have 3 samples for wild type and 1 ...
pietro_molina's user avatar
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328 views

Help with performing PCA analysis on data from 3 different datasets of normalized counts data for RNA-seq experiment

So, I have limited knowledge of R but I need to do a PCA analysis of 3 different datasets of gene expression as a result of combined growth or mono-culture growth. The 3 different datasets I performed ...
Justin1609's user avatar
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1 answer
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Understanding the different designs in DESeq2

I am using DEseq2 and trying to understand the results obtained using different models. I have a data design with 2 genotypes and 2 time points. ...
yathrakaaran's user avatar
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1 answer
232 views

Different contrasts in DESeq2

I have a treatment and control in two time points like this ...
Zizogolu's user avatar
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1 vote
2 answers
324 views

DEseq2 contrast in two time points

I need help with some clarifications please I have control versus treatment in two time points like ...
Zizogolu's user avatar
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213 views

Differential miRNA expression using RPM

I have microRNA (miRNA) expression data in RPM. I would like to do differential gene expression between two groups. How can I do this? I have considered edgeR and DESeq2 in R, but it looks like they ...
Sylvia Rodriguez's user avatar
-1 votes
1 answer
3k views

Adjusted P-value from DESeq2

What does the padj really mean? I believe it's a BH method, where it attempts to quantify the likelihood of a "false positive" but I am not sure. Also, what does it mean if the resulting ...
CodeMonke's user avatar
1 vote
1 answer
106 views

DESEQ2 Question about results()

I am currently learning to perform Differential Analysis via DESEQ2 R Package, and I believe I've made progress, able to format the data correctly [maybe] for DDS(). When I run the results function to ...
CodeMonke's user avatar
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2 answers
954 views

Beginner with DESeq2 having issue with analysis

I am trying to run DESeq2 analysis on my featureCounts output counts table. I ran the following code: ...
Justin1609's user avatar
1 vote
1 answer
460 views

DESeq2. Which is better: using the altHypothesis argument in the results function or manually filtering for your desired P-value and Log2FoldChange?

In DESeq2 you can identify your differentially expressed (DE) genes using the results function. I noticed people in my lab using the results() function with the minimum number of arguments supplied (...
Sam's user avatar
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2 votes
1 answer
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How does FDRtool work?

I have a question about using FDRtool. In the below code (on RNA seq data whose p values were acquired using Deseq2), the FDRtool was first used and thereafter p.adjust using the benjamini hochberg ...
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