Tag: enhancedVolcano

Forgive me if this post is messy, I’m new to this! I’m analyzing RNA Seq data and found that one of my samples is an outlier (sample AV17). I’m trying to exclude it from my analysis, but whenever I do, using this code: dds = subset(countData, select = -c(AV17) ),…

Hello everyone, I am an absolute beginner on sequencing analysis and DESeq2, so please forgive me for possibly mundane questions. I have tried to look up different methods, but couldn’t find a fitting answer yet. I am currently working with sequencing data derived from an Illumina sequencer. The data is…

DOI: 10.18129/B9.bioc.airway     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see airway. RangedSummarizedExperiment for RNA-Seq in airway smooth muscle cells, by Himes et al PLoS One 2014 Bioconductor version: 3.15 This package provides a RangedSummarizedExperiment object of read counts in genes for…

removeBatchEffect with non-linear model fit 0 @2289c15f Last seen 6 hours ago Germany Hello, I am attempting to use limma’s removeBatchEffect for visualization purposes (heatmat & PCA) while fitting non-linear models (splines) to my expression data in DESeq2. Given that my design is balanced, would this approach work within the…

Hi, I am hoping this isn’t a stupid question as I am really lost here. I have extensively read the manual and other forum posts but am struggling to find a solution. I am using DESeq2 to analyse my data set but running into problems with an interaction term in…

Hello, I am fitting splines in DESeq2 like so: dds <- DESeqDataSetFromMatrix(countData = counts, colData = coldata, design = ~ ns(age_scaled, df = 3)) Plotting later using the code Mike Love posted elsewhere: dat <- plotCounts(dds, gene, intgroup = c(“age”, “sex”, “genotype”), returnData = TRUE) %>% mutate(logmu = design_mat %*%…

DOI: 10.18129/B9.bioc.DESeq2   This is the development version of DESeq2; for the stable release version, see DESeq2. Differential gene expression analysis based on the negative binomial distribution Bioconductor version: Development (3.19) Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model…

Hello, I am running differential expression analysis on age-related changes in transcription using natural splines with DESeq2 like so: dds <- DESeqDataSetFromMatrix(countData = counts, colData = coldata, design = ~ ns(age_scaled, df = 3)) keep <- rowSums(counts(dds) >= 10) >= 3 dds <- dds[keep,] dds <- DESeq(dds, test=”LRT”, reduced =…

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Ágoston D, Baltás E, Ócsai H, Rátka S, Lázár PG, Korom I et al (2020) Evaluation of calcium electroporation for the treatment of cutaneous metastases: a double blinded randomised controlled phase II trial. Cancers. doi.org/10.3390/cancers12010179 Article  PubMed  PubMed Central  Google Scholar  Alrumaihi F (2022) The multi-functional roles of CCR7 in…

I’m using the EnhancedVolcano package in R to generate plots, which utilizes ggplot2 under the hood. When I try to save the plots at various dimensions using ggsave(), I’ve noticed that the text and titles remain the same size, causing the main plot contents to shrink and become less visible…

Tool:The script to install the required packages for gene expression analysis using DESeq2 for downstream analysis and visualization 0 if (!requireNamespace(“BiocManager”, quietly = TRUE)) install.packages(“BiocManager”) # Install Bioconductor packages BiocManager::install(‘DESeq2’) BiocManager::install(“apeglm”) BiocManager::install(“EnhancedVolcano”) BiocManager::install(“Glimma”) BiocManager::install(“ggrepel”) BiocManager::install(‘limma’) BiocManager::install(‘edgeR’) BiocManager::install(“reactome.db”) BiocManager::install(“AnnotationDbi”) # Install CRAN packages install.packages(‘tidyverse’) install.packages(‘ggplot2’) install.packages(“pheatmap”) R RNAseq installation DESeq2 •…

Tool:the script to install all the required packages for gene expression analysis using DESeq2 0 if (!requireNamespace(“BiocManager”, quietly = TRUE)) install.packages(“BiocManager”) # Install Bioconductor packages BiocManager::install(‘DESeq2’) BiocManager::install(“apeglm”) BiocManager::install(“EnhancedVolcano”) BiocManager::install(“Glimma”) BiocManager::install(“ggrepel”) BiocManager::install(‘limma’) BiocManager::install(‘edgeR’) BiocManager::install(“reactome.db”) BiocManager::install(“AnnotationDbi”) # Install CRAN packages install.packages(‘tidyverse’) install.packages(‘ggplot2’) install.packages(“pheatmap”) R RNAseq installation DESeq2 • 29 views Read more…

Dear Community,(Disclaimer : I learned R two weeks ago so most probably a very nooby question)I have run the follwing code to install DESeq2 based on the advice of my Post-Doc: BiocManager::install(c(“DESeq2″,”EnhancedVolcano”,”apeglm”)) Everything seemed fine except for DESeq2 where I had an issue with dependcy for the “RCurl” package that…

Hey, thanks for the comments. There is a somewhat indirect way of doing this by modifying the transparency of the points via colAlpha. Take a look: library(airway) library(magrittr) data(“airway”) airway$dex %<>% relevel(“untrt”) library(“DESeq2”) dds <- DESeqDataSet(airway, design = ~cell + dex) dds <- DESeq(dds, betaPrior = FALSE) res1 <- results(dds,…

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Hi everyone First of all thank you for making rna-seq data much more accessible to an average clinical doctor through the DEseq2 packages and vignettes. I am though running into some trouble: I have a dataset of Nanostring mRNA-data from clinical study, which later was followed up. I therefore have…

My Volcano plot is working fine for the argument on one shape for all as below; EnhancedVolcano(res_df, lab = res_df$gene_sym, x = ‘log2FoldChange’, y = ‘pvalue’, title=”MSC Cellular RNA vs MSC Exosome”, pCutoff = 0.05, FCcutoff = 1, pointSize = 3.0, labSize = 6.0, shape = 23, colAlpha = 1)…

EnhancedVolcano Labels 0 When using EnhancedVolcano, can I label a certain gene of interest using ‘selectLab’ while still labeling the genes that pass my thresholds? It seems that when I use selectLab I loose all the other red dots labels. Is there a way to keep them both? Kevin Blighe…

1. Introduction The synthesis of poly(ADP-ribose) (PAR) is an immediate response of cells to DNA damage catalyzed by poly(ADP-ribose) polymerases, which transfer ADP-ribose units from NAD+ onto target molecules [1]. PAR is a linear and branched polymer up to 200 units long that is covalently attached to the target proteins,…

Hi everyone, I would like to colour a specific population of genes in a volcano plot using enhanced volcano function. The thing is they are crowded in the rest of the non-significant genes. Would like to overlay them to be visible. Here is the code used keyvals.colour <- ifelse( res_table_tb_sex$ygenes…

Hi, I’m currently trying to assess fold change when comparing two different sample types using DESeq2 package and I’m getting weird Cook’s distance values which are causing major problems. The two different samples have different amounts of replicates (6 replicates vs 5 replicates) which might be the reason for these…

Help for RNA sequencing analysis with DESEQ2 0 @80066fff Last seen 1 day ago Canada Hello everyone, I’m currently trying to perform DESEQ2 with my own RNA sequencing results. I performed whole transcriptome RNA sequencing and the subsequent analysis I performed via galaxy. I performed first fastp on the samples,…

Sample preparation and sequencing The method of sample collection and processing is described in a companion article (ref. 23). Sequencing and basic bioinformatic processing of DNA-, RNA- and ATAC-seq data are included there as well. Gene expression normalization and filtering The number of non-ribosomal protein-coding genes on the 23 canonical chromosome pairs…

Hi, I have a question about DESeq2 LFCshrinkage: Is it possible that some genes have a slightly higher LFC after shrinkage? It happened during my RNAseq DE analysis, I have very deeply sequenced samples with large base means. I tried visualizing using MAplot check, and it looks fine. I’m mainly…

Showing : project • reset 1 result • Page 1 of 1 Recent … Replies Answer: merging VCF files by geweloy594 • 0 To merge multiple VCF files into a single VCF file, you can use VCF Merger software. This tool helps to merge numerous VCF data files and t……

Hi, I am working with a dataframe in R containing the quantitative data and trying to plot a volcano plot using library(EnhancedVolcano) package. I am currently analyzing by subsetting based on corresponding matching pairs of “Coef” and “P.value” obtained from limma (for instance; Coef.HC_6h_vs_0h and P.value.HC_6h_vs_0h) individually and export the…

GDCquery_Maf error 0 @76e1237b Last seen 1 day ago Singapore Hi all, I really need some help. I am trying to run GDCquery_Maf which worked fine until yesterday. Now I get the following error: Error in GDCquery(paste0(“TCGA-“, tumor), data.category = “Simple Nucleotide Variation”, : Please set a valid workflow.type argument…

circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data Introduction nf-core/circrna is a best-practice analysis pipeline for the quantification, miRNA target prediction and differential expression analysis of circular RNAs in paired-end RNA sequencing data. The pipeline is built using Nextflow, a workflow tool to run tasks across…

Hi All, So i an currently attempting to use Enhanced volcano to visualise a set of RNA-seq data, but when I run the below script, I get back the error message below. Does anyone know what the problem is – I can’t see anything wrong in the code. Error in…

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…

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…

I am making a volcano plot for my phosphoproteomics data and seemingly the data are not centered around the origin. The reason that I know there is something wrong is because before my code was producing the correct volcano plot, and now it is shifted. What are some reasons why…

DOI: 10.18129/B9.bioc.DESeq2     This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see DESeq2. Differential gene expression analysis based on the negative binomial distribution Bioconductor version: 3.10 Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on…

James W. MacDonald 57k 1 week, 5 days ago United States Answer: Biomart’s getBM returns no genes for an existing GO-term in grch38, and less the Michael Love 33k 1 week, 6 days ago United States Answer: Normalizing 5′ Nascent RNA-seq data to identify differentially expressed transcr Kevin Blighe 3.3k 2 weeks, 2 days ago Republic…