Tag: DESeq

Test if a gene is NOT differentially expressed in DESeq2?

Test if a gene is NOT differentially expressed in DESeq2? 1 @pennylane-21859 Last seen 1 day ago United States First, my apologies if this has been covered already. I thought for sure it would have been, but I can’t find the relevant info with my searches. It’s pretty obvious from…

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Large DE LogFC range

Large DE LogFC range 1 @3d20f23f Last seen 1 hour ago Italy I’m working with DESeq2 to make a DE analysis between samples in two different conditions. During the analysis, I identified a batch effect due to the sequencing time modelled as a covariate in the design formula. From the…

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Which method works best for analysing ONE sample of scRNA-seq data?

Which method works best for analysing ONE sample of scRNA-seq data? 1 Hello, I currently have a single-cell RNA-seq (scRNA-seq) data of a single person (sample) and i want to perform DE analysis. However, when I run the DESeq() in the DESeq2 package, it shows an error about only one…

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DE analysis model matrix for paired samples

DE analysis model matrix for paired samples 1 @tkapell-14647 Last seen 2 hours ago Helmholtz Center Munich, Germany Hi, I am analyzing a NanoString dataset where the metadata look as below: The factor of interest is the “group” and both groups are found in each mouse (“mouseID”) (paired samples). I…

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normalization for unsupervised analysis by DESeq2

normalization for unsupervised analysis by DESeq2 1 Hi friends I want to use DESeq2 to normalize the raw count data to do PCA. I dont have colData. What code should I use? because in the DESeq2 workflow we need colData and design. thanks RNA-Seq • 216 views • link updated…

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rna seq – How does DESeq2 “collapseReplicates” work on read counts data?

Comparing read counts from an RNA-seq experiment for a couple select genes before and after using DESeq2’s collapseReplicates function yields interesting results: Before: Geneid foo1.1 foo1.2 foo2.1 foo2.2 foo3.1 foo3.2 bar1.1 bar1.2 bar2.1 bar2.2 bar3.1 bar3.2 baz1.1 baz1.2 baz2.1 baz2.2 baz3.1 baz3.2 WASH7P 6 5 0 2 7 3 1…

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DESeq2 input from GDAC firehose

Hi guys, I hope you are fine. I’m not good in English so if you couldn’t understand my question, please feel free to reply. I’m a beginner of bioinformatics. I want to practice differential expressed gene (DEG) analysis in R. The RNA seq data I used was downloaded from broad…

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Strangely too low P-value and Adjusted P-value(FDR) DESeq2 and edgeR

My data is experimental data that has been overexpressed for a specific gene. Data samples are divided into 3 groups according to the over-expression time and each group has 3 samples. (total 9 samples) I conducted DGE analysis on the control group and one case group with DESeq2. cts <-…

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How does the DESeq2 work?

This is not DESeq2 specific but rather deals with modeling in general when comparing two groups. Whether you’re using DESeq2 or a t-test or some other linear model, you have to specify exactly what it is that you’re trying to model. If you assign some patients to a “treatment” group…

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downloading RNA seq data

downloading RNA seq data 0 Hi friends I am using the following code to get the data from TCGA. I want to have only one allocate of each person then I will have unique patients ID. Is there any line of code that I should add to this to get…

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Heatmap deseq2

I’m using deseq2 for DEA but when I create a heatmap with only DEGs, it looks very strange: I’m not sure whether there are only overexpressed genes or whether the dataset is not normalized properly. I probably made a mistake somewhere in my coding but I don’t know where to…

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DESeq2 analysis for targeted RNA-seq

Dear all, I am attempting to perform DESeq2 analysis (using the Geneious plugin) for targeted RNA-seq of several hundred genes. Only the target set of genes is sequenced, as the primer that I use for first strand cDNA synthesis is specific to the target set of genes. I have three…

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Immune-related Prognostic Genes of ccRCC

Introduction Kidney cancer is one of the most commonly diagnosed tumors around the globe.1 According to the statistics from the World Health Organization, annually, there are more than 140,000 RCC-related deaths.2 ccRCC is the most typical subtype of kidney cancer and contributes to the majority of kidney cancer-related deaths.3,4 Until…

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Bioconductor – derfinder (development version)

DOI: 10.18129/B9.bioc.derfinder     This is the development version of derfinder; for the stable release version, see derfinder. Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach Bioconductor version: Development (3.15) This package provides functions for annotation-agnostic differential expression analysis of RNA-seq data. Two…

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RNAseq using galaxy

RNAseq using galaxy 0 @e3a40d42 Last seen 1 hour ago United States I am new to rnaseq, I am using RNA star to map the genes and count reads per gene. After running the feature counts on RNA Star output, I will like to proceed to the deseq2 for differential…

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Bioconductor – TBSignatureProfiler (development version)

DOI: 10.18129/B9.bioc.TBSignatureProfiler     This is the development version of TBSignatureProfiler; for the stable release version, see TBSignatureProfiler. Profile RNA-Seq Data Using TB Pathway Signatures Bioconductor version: Development (3.15) Gene signatures of TB progression, TB disease, and other TB disease states have been validated and published previously. This package aggregates…

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Comparative de novo transcriptome analysis identifies salinity stress responsive genes and metabolic pathways in sugarcane and its wild relative Erianthus arundinaceus [Retzius] Jeswiet

1. Singh, A. et al. Phytochemical profile of sugarcane and its potential health aspects. Pharmacogn. Rev. 9, 45–54 (2015). CAS  PubMed  PubMed Central  Google Scholar  2. Eggleston, G. Positive aspects of cane sugar and sugar cane derived products in food and nutrition. J. Agric. Food Chem. 66, 4007–4012 (2018). CAS …

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Using DESeq2 to analyse multi-variate design resulting in testing the wrong parameter

Enter the body of text here Hi, I am analysing a RNA Seq dataset coming from 3 independent cell isolates (isolate1, isolate2, isolate3), each given 3 different treatments (control, drug1, drug2). We are testing drug 1 against control in the first instance: We also observed that there is some variation…

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sigh of log2FC values in DESeq2

sigh of log2FC values in DESeq2 0 @194b0276 Last seen 10 hours ago United States Can someone explain to me how is the sign of log2FoldChange is set in the results of DEseq2? I was pretty sure that it is calculated as log2(Counts_treatment/Count_reference), where reference is determined alphabetically (unless specified…

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featureCounts output has letters and +/- sign

featureCounts output has letters and +/- sign 1 Hello, I have created a featureCounts table and 10 of my files had weird outputs. Some values were my organism name and others were a “+” or “-“. I could not find anything about this in the manual. I tried to re-run…

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GeneTonic: an R/Bioconductor package for streamlining the interpretation of RNA-seq data | BMC Bioinformatics

1. Van den Berge K, Hembach KM, Soneson C, Tiberi S, Clement L, Love MI, Patro R, Robinson MD. RNA sequencing data: Hitchhikers guide to expression analysis. Annu Rev Biomed Data Sci. 2019;2(1):139–73. doi.org/10.1146/annurev-biodatasci-072018-021255. Article  Google Scholar  2. Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A,…

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weighted regression – Deriving initial weights for IRLS in DESeq2’s GLM model

In the paper introducing DESeq2 they say: As the GLM’s link function is $g(mu) = log (mu)$ and its variance function is $V( mu; alpha) = mu + alpha mu^2$, the elements of the diagonal matrix $W_i$ are given by $$w_{jj} = frac{1}{g^{prime}(mu_j)^2 V(mu_j)} = frac{1}{frac{1}{mu_j}+alpha}$$ While I am not…

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Unlog transformed data in DESeq2

Unlog transformed data in DESeq2 1 @mohammedtoufiq91-17679 Last seen 13 hours ago Qatar Hi, I am using DESeq2 for analyzing Illumina RNASeq datasets. I follow the below steps; Derived raw counts (from featureCounts) > Imported counts to DESeq2 Normalised the counts via an estimation of size factors (counts(dds, normalized =…

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Analyzing RNA-seq data with DESeq2 Tutorial

I am working through the Analyzing RNA-seq data with DESeq2 tutorial, and running it through RMarkdown. Loading the tximeta package in the tutorial code below: coldata <- samples coldata$files <- files coldata$names <- coldata$run library(“tximeta”) # se <- tximeta(coldata) # ddsTxi <- DESeqDataSet(se, design = ~ condition) Is causing the…

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DESeq2 comparisons using contrast

DESeq2 comparisons using contrast 0 Hi all, I recently started analyzing some bacterial RNAseq data. So, I have 4 different strains and for each strain I have 2 conditions. Let’s say strains are A, B, C and D while conditions are X and Y. I have a total of 24…

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No differentially expressed genes

Hi, I have a dataset now with 36k lncRNAs and I’m using DESeq2 to find differentially expressed lncRNAs between a healthy group and a disease group, but unfortunately I cannot find any DE lncRNAs with low padj values. However, when I explore my data by taking the log2 fold change…

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batch, condition and tissue information

Hi all, I have the following type of data: 5 batches (5 different data sets) 2 conditions (wt, mutant) 3 different tissues (data 1 and 2 represent tissue 1, data 3 and 4 represent tissue 2, data 5 represents tissue 3) I would like to find DEGs in tissue 1…

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dispersion of a gene, what does it mean?

dispersion of a gene, what does it mean? 2 In all RNA-seq analysis applications they talk about the dispersion of a gene. As far as I understood, it is not a variance of the normalized counts for a given gene. It is somehow much more complicated. DESeq defines the dispersion…

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get rRNA FASTA file for a particular bacteria

get rRNA FASTA file for a particular bacteria 0 Hey all, I was trying to find a way to get all rRNA (5S, 16S and 23S) FASTA sequences for a particular bacteria (B. thetaiotaomicron VPI-5482, which is the type strain). I wanted this file so that I could use something…

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Virtual environment in R? – Stackify

I’m going to use the comment posted by @cboettig in order to resolve this question. Packrat Packrat is a dependency management system for R. Gives you three important advantages (all of them focused in your portability needs) Isolated : Installing a new or updated package for one project won’t break…

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Diffbind3 dba.plotMA error

Hello, I am analyzing some ATAC-seq from flies using Diffbind3.0.8 and EdgeR. I initially ran dba.analyze() with the default peak size of 401 and was able to graph the results using dba.plotMA and dba.plotVolcano when my contrasts were evaluated using both EdgeR and DESEQ2. After resizing the peaks to 100…

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Design formula in DESeq2

Hello, I am using DESeq2 for analysis of RNAseq data. I would like to ask you about the design in the DESEq2 formula. I have tissue from animals treated with a chemical and my animal model is a colorectal cancer model. My variables are gender (male or female), treatment (treated…

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How to get normalized count table from DESeq?

How to get normalized count table from DESeq? 1 Hi, I’m using Deseq compare differential abundance. Here is my code: ds.all <- phyloseq_to_deseq2(ps0.infant.pbs, ~ sample_type) geoMeans <- apply(counts(ds.all),1,gm_mean) ds.all <- estimateSizeFactors(ds.all,geoMeans = geoMeans) dds.all <- DESeq(ds.all,fitType = “local”) Then as the results I got 8 ASVs that showed significantly different….

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Assigning Object to Function Rather than vice-versa?

R Syntax Clarification in DeSeq2 Vignette: Assigning Object to Function Rather than vice-versa? 1 Hi, I have a question about some of the R syntax present in the DeSeq2 vignette. The following comes directly from the section regarding the removal of batch effects: mat <- assay(vsd) mm <- model.matrix(~condition, colData(vsd))…

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Combining Microarray and RNA-Seq datasets visualization and comparison

Combining Microarray and RNA-Seq datasets visualization and comparison 0 Hi, I am working with some public transcriptomics datasets (both Microarray and RNA-Seq) to study gene signatures of bacterial “Infected” samples vs. Healthy Control samples. The starting point of analysis of Microarray data is .CEL files for Affymetrix (normalize using GCRMA)…

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different results between DESeq model with multiple groups or with specific groups

different results between DESeq model with multiple groups or with specific groups 1 @b295d7f1 Last seen 3 hours ago Italy Hi! I am working with DESeq2 to perform a differential expression analysis between different treatments.I have 4 conditions and 4 four biological replicates for each conditions. I’ve performed differential expression…

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TCGA dataset normalization

TCGA dataset normalization 0 hi. i am new to machine learning. i want to normalize my data which I downloaded from UCSC Xena browser for pancreatic cancer TCGA PAAD is its id. when I try to run this code it is showing error given below library( “DESeq2” ) library(ggplot2) countData…

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Transposition and duplication of MADS-domain transcription factor genes in annual and perennial Arabis species modulates flowering

Annual and perennial species occur in many plant families. Annual plants and some perennials are monocarpic (flowering once in their life cycle), characterized by a massive flowering and typically produce many seeds before the whole plant senesces. By contrast, most perennials live for many years, show delayed reproduction, and are…

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Understanding output of Negative Binomial in DESeq2

Enter the body of text here Dear author and seniors, Hope you all are doing great. I am very new to RNASeq and DESeq2. I know that the negative Binomial (Gamma Poisson) is used to fit this RNAseq count data. All genes are assessed/fitted between two conditions and we get…

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DEseq2 in R studio Cloud – RStudio Cloud

Dear all, I am investigating the possibility of using RStudio Cloud to teach RNA sequencing technologies using the DESeq2 package. Bioconductor DESeq2 Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. My attemps to compile…

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Aro Biotherapeutics hiring Investigator, Genetics & Bioinformatics in Philadelphia, Pennsylvania, United States

About Aro BioTx Join the team at Aro Biotherapeutics creating breakthrough biotherapeutics based on Centyrin oligonucleotide conjugates. Centyrins are small protein domains based on the fibronectin domains of human Tenascin C that combine the affinity and specificity properties of antibodies with the stability and tissue penetration properties of small molecules….

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Bioconductor – ERSSA

DOI: 10.18129/B9.bioc.ERSSA     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see ERSSA. Empirical RNA-seq Sample Size Analysis Bioconductor version: 3.9 The ERSSA package takes user supplied RNA-seq differential expression dataset and calculates the number of differentially expressed genes at varying biological replicate…

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Bioconductor – NBAMSeq

DOI: 10.18129/B9.bioc.NBAMSeq     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see NBAMSeq. Negative Binomial Additive Model for RNA-Seq Data Bioconductor version: 3.9 High-throughput sequencing experiments followed by differential expression analysis is a widely used approach to detect genomic biomarkers. A fundamental step…

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Homer finds same peak multiple times

I am using Homer to identify peaks in RNA-seq data and then determine differential expression by counting reads per peak. Homer has a lovely package that does just this: getDifferentialPeaksReplicates.pl. The issue is that for some reason Homer returns the same peak multiple times in its final output (Bonus question:…

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Understanding the output of Negative Binomial in DESeq2

Are zero is a default option of log2fold change to be considered as up and down? Yes, by default, the null hypothesis is that the log2FoldChange is zero. Does this mean that there are seven genes in total that will have significant adjusted p-value? Yes, you are interpreting your results…

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Exporting normalized counts data from DeSeq2

Exporting normalized counts data from DeSeq2 1 Hi, I am working with large RNA-Seq dataset downloaded from the NCBI GEO. I would like to export the normalized counts data from DeSeq2 based on size factor normalization for further downstream analysis. It seems like running dds <- DESeq(dds) and dds <-…

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DESEQ2 / OUTRIDER Error

DESEQ2 / OUTRIDER Error 0 I’m using OUTRIDER, which I understand is very similar in terms of initial data object creation to deseq2. the OUTRIDER datasets are the same in structure as deseq datasets. In my analysis, I’m receiving the following error at some stage “Error in estimateSizeFactorsForMatrix(fcMat) : every…

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DESeq2 errors for RNA-SEQ data analysis in R studio

Hi All, I am getting an error msgs while running DESeq2 Bioconductor in R studio. When I tried without using the gene_ID column and it does work but then I am unable to see which genes are DEGs. My Input file: gene_ID t1.control t2.control t3.control t4.sample t5.sample t6.sample ENSCAFG1 363…

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Determining up-regulation vs down-regulation DESeq2 likelihood ratio test

Determining up-regulation vs down-regulation DESeq2 likelihood ratio test 0 Hello, I am hoping to receive some guidance on interpreting an RNA-sequencing project I am conducting. For this project, I have 9 time points, 3 biological replicates per time point, and 2 genotypes: wildtype vs mutant. I am using a likelihood…

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Bug#994443: r-bioc-deseq2: autopkgtest regression

Source: r-bioc-deseq2 Version: 1.30.1+dfsg-1 Severity: serious X-Debbugs-CC: debian…@lists.debian.org User: debian…@lists.debian.org Usertags: regression Hi Maintainer The autopkgtests of r-bioc-deseq2 regressed in testing sometime after 2021-09-07 11:35:05 UTC [1]. E: Package ‘r-bioc-tximportdata’ has no installation candidate pkg-r-autopkgtest FAIL badpkg blame: r-bioc-deseq2 I suspect this is due to #961138. Regards Graham [1] ci.debian.net/packages/r/r-bioc-deseq2/testing/amd64/

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DESeq2 log2FC and p-value filtering

DESeq2 log2FC and p-value filtering 1 Dear all, I want to filter DE genes by log2FC > 2/-2 and p-value 0.0001. Why this two versions of lof2FC and p-value filtering differ in up- and down-regulated genes numbers (from 800 to 1500) and which one is the right one ? 1….

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rna seq batch effects and cross species study

rna seq batch effects and cross species study 1 hi I am doing an expression analysis of rna seq dataset I have some doubts to be clarified can we do an analysis by choosing controls and test from two different datasets? One of the rna seq dataset is human(test is…

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Correct way to make multiple comparisons on DESeq2?

I have a project where I have done RNA-seq (paired-end sequencing on Illumina HiSeq) of a worm at different days of development i.e. Ages 0-12. For each age, I have sequenced 3 replicate specimens. I’m new to DESeq2 and I was wondering if what I did below is correct. library(DESeq2)…

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Bioconductor – TBSignatureProfiler

DOI: 10.18129/B9.bioc.TBSignatureProfiler     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see TBSignatureProfiler. Profile RA-Seq Data Using TB Pathway Signatures Bioconductor version: 3.12 Signatures of TB progression, TB disease, and other TB disease states have been created. This package makes it easy to…

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how to save zero counts on normalization step

Deseq2 – how to save zero counts on normalization step 0 Hi all, I have raw read counts [of rna-seq]. I need to normalize this data and have done it using DESeq2. But, I found that DESeq2 eliminates the read counts of genes when it’s equal to 0. I don’t…

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Making a heatmap: sample vs. fold change

Making a heatmap: sample vs. fold change 1 Hello, I often see in RNA-Seq papers a figure that plots samples on the Y axis, genes on the X axis, and a fill color representing fold change. Here is an example. The DESeq package explains how to make a heatmap of…

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Plot LFC with pheatmap of differentially expressed gene list from DESeq2.

Hi, all! First post, so apologies for any flaws with post structure. I am attempting to make a basic heatmap that shows the log fold change of differentially expressed genes, as identified by DESeq2. See below the code I am using for DESeq2: ##Load DESeq2 source(“https://bioconductor.org/biocLite.R”) biocLite(“DESeq2”) biocLite(“stringi”) biocLite(“MASS”) install.packages(“survival”)…

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desEQ2 eRROR

I have count matrix from feature count with gene_names for each sample. When I am using DESeqDataSetfromMatrix with the following commands: count <- read.csv(“matrix.count”, header = TRUE, row.names = 1, sep =’t’) info <- read.table(“coldata2.txt”, header = TRUE, sep =’t’) library(DESeq2) library(apeglm) ds <- DESeqDataSetFromMatrix(count, info, ~condition) Error: DESeqDataSet(se, design…

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DESeq2 treated vs untreated and contrast vs no contrast

DESeq2 treated vs untreated and contrast vs no contrast 0 Dear all, I have two RNAseq data with 4 different treatments run in 2017 (Let’s say treatment A and B) and 2019 (Treatment C and D); those have two different read lengths (I read for DE it does not matter…

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Kallisto Bootstrapping and deseq2

Kallisto Bootstrapping and deseq2 0 Dear all, Just a quick clarification about importing pseudocounts into the deseq2 package. I don’t usually apply the bootstrapping step with the Kallisto package for deseq2 analysis. My results are definitely comparable to ones generated by technicians in my university with totally different approaches. Nevertheless,…

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Disabling de novo DNA methylation in embryonic stem cells allows an illegitimate fate trajectory

The mammalian genome is characterized by widespread methylation of cytosine residues. After fertilization, however, both maternal and paternal genomes undergo extensive demethylation, reaching a low point in the blastocyst (1⇓⇓–4). The embryo genome is then remethylated by the activity of de novo DNA methylation enzymes (5). Mouse embryonic stem (ES)…

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Accepted r-bioc-deseq2 1.32.0+dfsg-1 (source) into unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Tue, 14 Sep 2021 00:18:17 +0530 Source: r-bioc-deseq2 Architecture: source Version: 1.32.0+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian R Packages Maintainers <r-pkg-t…@alioth-lists.debian.net> Changed-By: Nilesh Patra <nil…@debian.org> Changes: r-bioc-deseq2 (1.32.0+dfsg-1) unstable; urgency=medium . [ Andreas Tille ] * Team Upload. * New…

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DGE from tumor-adjacent normal pair RNA-seq data. For an individual, no replicate

Single sample analysis can be done in edgeR, while it is deprecated in DNASeq2 in 2018 probably (if you can use old DESeq version then it will work in single sample also). For egdeR you just do library(edgeR) setwd() rawdata <- read.delim(“filename”, check.names=FALSE, stringsAsFactors=FALSE) ngenes <- 10000 #no. of genes…

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Outliers on DESEq2 Results

I have an RNAseq dataset, where one of the genes I intend to analyze has hundreds of counts ranging from 10 to 12, with a few counts > 9000. I process this data in Deseq2 and get that the gene is differentially expressed across several samples of interest. What can…

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Gene with hundreds of counts very similar, is it possible to use it to get DEGs?

Gene with hundreds of counts very similar, is it possible to use it to get DEGs? 0 Hi, I’m starting in boinfomatics and I’m using Deseq2 for differential expression analysis. I have an RNAseq dataset, where one of the genes I intend to analyze has hundreds of counts ranging from…

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Warning messages on Apple M1 BigSur

Warning messages on Apple M1 BigSur 0 @095e334e Last seen 4 hours ago Hong Kong Hi, Does bioconductor supports the binary of R created specifically for arm chips already ? I get the following warning when trying to install any Bioconductor packages: 1: In .inet_warning(msg) : unable to access index…

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small dimensions in the matrix of counts from smallRNA using DESEq2

small dimensions in the matrix of counts from smallRNA using DESEq2 1 @andreia-23745 Last seen 8 hours ago Portugal Hi there, I am doing smallRNA data analysis and I have a matrix of counts 17 miRNA and 16 samples I wonder if its correct to perform the results() from DESeq2…

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Normalization and differential analysis in ATAC-seq data

Normalization and differential analysis in ATAC-seq data 2 Hello everyone! I would like to know if someone had experiences with normalization and differential expression on ATAC-seq data. After using MACS2 for the peak calling, how can we use Dseq2 or EdgeR on these datas? Someone try this? What is the…

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Statistics on RNAseq data

Statistics on RNAseq data 2 Hi I would like to know whether you can do statistical tests (e.g. ANOVAS etc.) on the TPM/RPKM counts of RNAseq data? Thanks on Statistics data RNAseq • 58 views This is not recommended due to a few underlying problems with RNA-seq data that include…

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‘package ‘limma’ could not be loaded’

trinity run_DE_analysis.pl Failed with error: ‘package ‘limma’ could not be loaded’ 1 Hi Experts, can someone please help me with this error while running run_DE_analysis.pl for DESeq2 analysis Loading required package: edgeR Loading required package: limma Error: package or namespace load failed for ‘limma’: .onLoad failed in loadNamespace() for ‘limma’,…

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DESeq2 normalization – Found Difference in values when calculated manually

DESeq2 normalization – Found Difference in values when calculated manually 0 Hi All, I learnt about how DESeq2 normalises the raw read counts in statquest. It was very helpful and I tried to repeat the steps for my sample data. But I am getting the output with minor difference –…

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Cutoff value for shrunken logFC

Cutoff value for shrunken logFC 0 Hello Is there any rule of thumb for filtering shrunken logFC, similar to |logFC|>1.5 for raw results? Or perhaps one should find the cutoff purely based on the distribution of shrunken logFC? I think some standardized value is needed though, e.g. from the perspective…

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DESeq2 Not full Rank – Age & Medication

DESeq2 Not full Rank – Age & Medication 0 Hi. I’ve a data matrix which looks like this: I’m trying to carrying out DGE analysis controlling for age and medication so I used the following: design(ddsMF)<-formula(~age+medication+group) ddsMF<-DESeq(ddsMF) And end up with the error, “Full model matrix is less than full…

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DESeq2

DESeq2 1 If deseq2 is used to analyze the differentially expressed gene, what is the effect of outliers on the results of DEGs? DEGs • 54 views DESeq2 detects automatically count outliers using Cooks’s distance and removes these genes from analysis. It also automatically removes genes whose mean of normalized…

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Need help to remove NA values from data frame

Need help to remove NA values from data frame 2 I have this data frame : and I want to remove those rows which contain NA values from the log2fold change column How can I do this through R? DeSEQ2 R • 256 views Hi Anas, If your data frame…

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low number of significant peaks for one contrast

I am using Diffbind to call differential peaks on an ATAC seq dataset of four conditions (AW, BW, B, and C), and each condition has 2 replicates. One of my replicates (BW2) has low quality (low number of peaks detected by MACS2 compared to the other replicate, and low FRiP)….

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ANOVA for RNA-seq data?

ANOVA for RNA-seq data? 2 Hello I have seem some platforms such as GEPIA offering ANOVA for differential gene expression analysis. However, as far as I’m concerned, ANOVA compares the averages and assumes equal distribution and variance among samples, which, as far I have been lead to assume, is uncommon…

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Filtering relevant Gene Ontology (GO) results from Gene Set Enrichment Analysis (GSEA)

Filtering relevant Gene Ontology (GO) results from Gene Set Enrichment Analysis (GSEA) 1 Hi all, I am new to bioinformatics and am currently learning how to use GSEA. Background: I analyzed my RNA-Seq results using DESeq2, and am now learning to perform GSEA. For my project, in broad terms, I…

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Comparing ribo-minus and polyA-selected RNAseq data

Comparing ribo-minus and polyA-selected RNAseq data 0 Hi, I’d like to compare two publicly available datasets that differ in the library prep method, and probably less importantly- read length. I am relatively inexperienced with RNAseq data analysis. bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1714-9#Sec8 This is the only piece of work I’ve found that tackles this…

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Replacing default numbers with geneNames in enhancedVolcano

Replacing default numbers with geneNames in enhancedVolcano 0 Hi Kevin, I am trying to plot a volcano plot with my DESeq2 results. I managed to get it working with most of the files, but I cant get rid of the default row numbers and replace it with geneName. Any help…

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ENHANCED GRAVITROPISM 2 encodes a STERILE ALPHA MOTIF–containing protein that controls root growth angle in barley and wheat

    Significance To date, the potential of utilizing root traits in plant breeding remains largely untapped. In this study, we cloned and characterized the ENHANCED GRAVITROPISM2 (EGT2) gene of barley that encodes a STERILE ALPHA MOTIF domain–containing protein. We demonstrated that EGT2 is a key gene of root growth…

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Comparing two conditions within multiple different groups with unequal sizes in DESeq

Comparing two conditions within multiple different groups with unequal sizes in DESeq 0 Hello, I have two conditions (condition A and condition B) and 4 groups (group 1, group 2, group 3). I want to compare condition A to condition B within each of the groups, performing differential expression analysis…

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Clustering without having any replication

Clustering without having any replication 1 I have raw read counts of three different samples (sub-types) with no replications like this > head(oc) sample1 sample2 sample3 WASH7P 3 29 48 MIR6859-1 0 6 4 DDX11L17 0 2 2 WASH9P 3 92 101 MTND1P23 8 154 139 MTND2P28 3104 3491 3814…

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RPKM and differential expression analysis

RPKM and differential expression analysis 1 Hello all, I am trying to analyse differential expression in a dataset for which I only have RPKM values available to me. I usually use the R/BioC environment for RNA-seq analysis, and have read in various BioC documentation that using RPKM values in packages…

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Benchmarking different DESeq2 design models

Benchmarking different DESeq2 design models 1 Hello, I have RNA time-course data and am looking to benchmark two different DESeq2 models I want to use. One design models time as a categorical variable, while the other design models time as a continuous variable. I am wondering if anyone knows of…

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gct output in DESeq2

gct output in DESeq2 2 Hi everyone, I’m trying to analyze my counts data with DESeq2 and based on the tutorial of GSEA, DESeq2 has an output format that can be used directly in the GSEA (here). However, I’m reading their workflow and I don’t find how to make this…

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No such file or directory when downloading DESeq2 package

error: cannot execute ‘f951’: execvp: No such file or directory when downloading DESeq2 package 0 @8e03f28b Last seen 4 hours ago United States When I download a package (DESeq2) from Bioconductor, I got the following error: gfortran: fatal error: cannot execute ‘f951’: execvp: No such file or directory compilation terminated….

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normalising Biological replicates for differential analysis

normalising Biological replicates for differential analysis 1 @f4d593ce Last seen 1 day ago I am new to DESEQ2 and RNA quantification and analysis in R. I have been given a dataset of 60k rows (of genes) and16 columns for 4 treatment conditions comprising of 4 repeat cell sample each. I…

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DESeq2 analysis example, opinions?

Hello everyone, Purpose of the analysis: In there a difference between TOV21G-PacR and TOV21G-cont, and between the PacR and cont? My question is if this analysis makes sense for you? I am analyzing this particular gene set (GSE172016). Within the data there are two cell lines (“OVCAR3” and “TOV21G”) and…

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More results when prefiltering in DESeq2

More results when prefiltering in DESeq2 0 Hello community, I have been using deseq2 for a while now and as is written in the tutorial, prefiltering is only necessary because of computational power since the results function applies the appropriate filtering. I have noticed that doing my analysis both ways,…

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r – How to replace row names in DESeq2 rlogTransformation matrix with actual gene name info present on another sheet?

I’m new to R and DESeq2 and I’m trying to run differential expression as below library(DESeq2) count_file_names <- grep(“counts”,list.files(“HTSeq_counts”),value=T) host_type < c(“Damaged”,”Control”) sample_information <-data.frame(sampleName = count_file_names, fileName = count_file_names, condition = host_type) DESeq_data <- DESeqDataSetFromHTSeqCount(sampleTable = sample_information, directory = “HTSeq_counts”, design = ~condition) colData(DESeq_data)$condition <- factor(colData(DESeq_data)$condition,levels = c(‘Damaged’,’Control’)) rld <-…

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How to replace row names in DESeq2 rlogTransformation matrix with actual gene name info present on another sheet?

I’m new to R and DESeq2 and I’m trying to run differential expression as below library(DESeq2) count_file_names <- grep(“counts”,list.files(“HTSeq_counts”),value=T) host_type < c(“Damaged”,”Control”) sample_information <-data.frame(sampleName = count_file_names, fileName = count_file_names, condition = host_type) DESeq_data <- DESeqDataSetFromHTSeqCount(sampleTable = sample_information, directory = “HTSeq_counts”, design = ~condition) colData(DESeq_data)$condition <- factor(colData(DESeq_data)$condition,levels = c(‘Damaged’,’Control’)) rld <-…

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How can I use R to do many genes survival analysis at the same time?

How can I use R to do many genes survival analysis at the same time? 1 I plan to use the DESeq2::rlog transformed TCGA HTseq_counts data and the TCGA clinical data to do survival analysis. But I am confused how to do many genes(>10000) survival analysis at the same time….

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Analysis of shRNA/CRISPR screens in 2021

I’ve used Mageck for CRISPR screens and it works great. A few things: It, by default, doesn’t allow mismatches between read and library but still I’ve always had good (>= ~80%) mapping rates; I’ve had better mapping results with paired-end reads (because if one read fails to align because of…

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pughlab/inspire-genomics: Pan-cancer analysis of genomic and immune landscape profiles of metastatic solid tumors treated with pembrolizumab

Contents Serial circulating tumor DNA (ctDNA) monitoring is emerging as a non-invasive strategy to predict and monitor immune checkpoint blockade (ICB) therapeutic efficacy across cancer types. Yet, limited data exist to show the relationship between ctDNA dynamics and tumor genome and immune microenvironment in patients receiving ICB. Here, we present…

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Differential Gene Expression

Can you analyze in GEO2R? => No, because this is RNA-seq and not microarrays. You are lucky thought that the authors seem to provide raw counts so you can easily fede them into DESeq2. Here is a code suggestion, for details please read the DESeq2 vignette extensively, it contains answers…

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How to calculate dispersion DESeq2

How to calculate dispersion DESeq2 – Step by Step 1 @gordon-smyth Last seen 8 hours ago WEHI, Melbourne, Australia The formula you quote is for the edgeR package rather than for DESeq2. The articles you cite are for three different packages. I doubt very much that you can compute the…

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How to write design and contrast in DESeq2 to find the up-regulated genes where the design have interactions

How to write design and contrast in DESeq2 to find the up-regulated genes where the design have interactions 0 Hello I have the following design in DESeq2: ~GT+TP+TP:GT . GT has two levels (K,W) . TP has two levels (0,2). I am looking for the genes that are up-regulated in…

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DESeq2 Model Design for Biological Replicates nested within Donor Replicates nested Within groups

Hello all, First time posting so apologies in advance if I missed any guidelines after reading through the posting guide. I have a question pertaining to model design for DESeq2 with nested “replicates”. I’ve read through this post as well as this relevant section in the DESeq2 vignette as well…

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Can I remove the control in differential expression analysis?

Hi there, Essentially, my experimental design is control vs treatment. Cells were sorted based on fluorescence, so there are 4 different “colors” of treated cells, i.e. red, green, green+red, and blue+green+red. I am interested in how the colors differ from one another. And, I have duplicates for all colors and…

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