Tag: LIMMA

[BioC] limma, remove two type of batch effect

Hi All, In my analysis, I want to find the different expression genes betweendissese A and B. There are two type of batch effect in my analysis. Iwant to use limma to remove two type of batch effect, one is gender,another is tissue type. I do as fellow. But I…

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CRAN Package Depends on Bioconductor Package Installing error

In R 3.0.2, the following works: At the time of this writing, the value ind can take a vector with values between 1 and 8, and the following meaning: 1: CRAN 2: BioC software 3: BioC annotation 4: BioC experiment 5: BioC extra 6: Omegahat 7: R-Forge 8: rforge.net This…

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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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Identification of differentially expressed genes in AF

Defeng Pan,1,* Yufei Zhou,2,* Shengjue Xiao,1,* Yue Hu,3,* Chunyan Huan,1 Qi Wu,1 Xiaotong Wang,1 Qinyuan Pan,1 Jie Liu,1 Hong Zhu1 1Department of Cardiology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, 221004, People’s Republic of China; 2Department of Cardiology, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital and Institutes of…

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Bioinformation Analysis Reveals IFIT1 as Potential Biomarkers in Centr

Introduction Tuberculosis (TB) is considered to be one of the top ten causes of death in the world, about a quarter of the world’s population is infected with M. tuberculosis.1 The World Health Organization (WHO) divides tuberculosis into pulmonary tuberculosis (PTB) and extra-pulmonary tuberculosis (EPTB). Although breakthroughs have been made…

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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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No results when inputting genes with scores

Hi, I am using EnrichR to analyze my DEGs gotten from limma. I extracted subsets of significant DEGs with their IDs and t-statistics that have been scaled, like the following example: CHI3L1 1.0000000 ARPC1B 0.9605097 SH3D21 0.9303946 FCGBP 0.9165999 MFNG 0.8830144 C2 0.8153162 CTA-398F10.2 0.8459803 CTSD 0.7543101 GRN 0.7503898 CTSB…

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Bioconductor – bnem (development version)

DOI: 10.18129/B9.bioc.bnem     This is the development version of bnem; for the stable release version, see bnem. Training of logical models from indirect measurements of perturbation experiments Bioconductor version: Development (3.15) bnem combines the use of indirect measurements of Nested Effects Models (package mnem) with the Boolean networks of…

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“Paired-end reads were detected in single-end read library”

“Paired-end reads were detected in single-end read library” 0 @9cb59de3 Last seen 12 hours ago United States Hello, I am using “featureCounts” in Rsubread package for analyzing bulk RNA-seq of drosophila. Since there is no inbuilt annotations of drosophila, I am trying to use a gtf file in the homepage…

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CASP5 and CR1 as potential biomarkers for Kawasaki disease: an Integrated Bioinformatics-Experimental Study

This article was originally published here BMC Pediatr. 2021 Dec 11;21(1):566. doi: 10.1186/s12887-021-03003-5. ABSTRACT BACKGROUND: Kawasaki disease (KD) is a pediatric inflammatory disorder causes coronary artery complications. The disease overlapping manifestations with a set of symptomatically like diseases such as bacterial and viral infections, juvenile idiopathic arthritis, Henoch-Schönlein purpura, infection…

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Prognosis Biomarkers via WGCNA in HCC

Introduction According to the cancer statistics reported in 2020, hepatocellular carcinoma (HCC) is the main type of Primary Carcinoma of the Liver and the second leading causes of cancer-related death globally, with a five-year survival rate < 20%.1 Currently, surgical resection, a standard therapy for HCC, contributes to the prognosis…

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Bioconductor – MSstats

    This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see MSstats. Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments Bioconductor version: 3.4 A set of tools for statistical relative protein significance analysis in DDA, SRM and DIA…

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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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Identification of lipid metabolism-associated gene signature

Background Female breast cancer has surpassed lung cancer as the most commonly diagnosed cancer. Despite the dramatic improvement in breast cancer prognosis due to recent therapeutic advances, such as more effective adjuvant and neo-adjuvant chemotherapies, together with more radical and safer surgery, advances in early diagnosis and treatment over the…

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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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normalize Input with Immunoprecipitated raw counts or not

RIP-seq : normalize Input with Immunoprecipitated raw counts or not 0 Hi everyone, I am analyzing a RIP-seq experiment made of 12 RNA libraries as follows : 6 “control” libraries : 3 input (total RNA) and their corresponding immunoprecipitated RNAs (IP) and 6 “affected” libraries : 3 input (total RNA)…

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Why there are same name with different value in my microarray result?

Why there are same name with different value in my microarray result? 0 I have done one color agilent microarray. I am processing my data, but my data showed one miRNA present in more than one place with different value. Could someone please tell me what is the reason for…

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How can we compare EdgeR to limma-voom?

How can we compare EdgeR to limma-voom? 0 Hi all, I did all my RNA-seq analysis for 500 patients with the EdgeR workflow as described in the manual. Now I read an article (F1000 research) where they state that EdgeR is mostly preferred in low-count situations, where limma-voom is recommended…

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Bioconductor – Harman

DOI: 10.18129/B9.bioc.Harman     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see Harman. The removal of batch effects from datasets using a PCA and constrained optimisation based technique Bioconductor version: 3.12 Harman is a PCA and constrained optimisation based technique that maximises the…

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limma+voom flips the sign of the effect from CPM?

limma+voom flips the sign of the effect from CPM? 0 Hello, I’m having a hard time figuring out how limma can switch the sign of an effect compared to the raw cpm or log2(cpm) values. In the figure below, I’m showing 4 genes (2×2 matrix) in our data compared between…

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Bioconductor – marray

    This package is for version 2.13 of Bioconductor; for the stable, up-to-date release version, see marray. Exploratory analysis for two-color spotted microarray data Bioconductor version: 2.13 Class definitions for two-color spotted microarray data. Fuctions for data input, diagnostic plots, normalization and quality checking. Author: Yee Hwa (Jean) Yang…

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voom mean-variance plot has set of genes where variance increases with expression level

voom mean-variance plot has set of genes where variance increases with expression level 0 I’m using limma + voom to model an expression dataset, but I’m observing a weird subset of genes where the standard deviation increases with the expression level rather than decreasing as is the case for most…

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Creating Heatmaps Of Diffrentially Expressed Genes In Angilent Single-Color Array Analysis

Creating Heatmaps Of Diffrentially Expressed Genes In Angilent Single-Color Array Analysis 0 I am using limma to analyze Agilent’s single color arrays to find differentially expressed genes, using the following procedure. targets <- limma::readTargets(“targets.txt”) project <- limma::read.maimages(targets,source=”agilent”, green.only=TRUE) project.bgc <- backgroundCorrect(project, method=”normexp”, offset=50) project.NormData <-normalizeBetweenArrays(project.bgc,method=”quantile”) design <- paste(targets$Target, sep=””) design…

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Bioconductor – ChIPComp

    This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see ChIPComp. Quantitative comparison of multiple ChIP-seq datasets Bioconductor version: 3.4 ChIPComp detects differentially bound sharp binding sites across multiple conditions considering matching control. Author: Hao Wu, Li Chen, Zhaohui S.Qin, Chi Wang Maintainer:…

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Classifiers for predicting coronary artery disease

Introduction Coronary artery disease (CAD) is a complex pathology associated with behavioral and environmental factors.1–3 CAD shows high prevalence and is associated with a high fatality rate among cardiovascular diseases. The main manifestations of CAD are stable or unstable angina pectoris and identifiable or unrecognized myocardial infarction.4 The main risk…

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Bioconductor – Ringo

DOI: 10.18129/B9.bioc.Ringo     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see Ringo. R Investigation of ChIP-chip Oligoarrays Bioconductor version: 3.9 The package Ringo facilitates the primary analysis of ChIP-chip data. The main functionalities of the package are data read-in, quality assessment, data…

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Batch correction for DE analysis

Batch correction for DE analysis 0 Hi, I have tried DE analysis using total and mRNA seq data (5 total RNA data and 5 mRNA data) and making the MDS plot in which 5 total RNA data are included in 2 groups (A, B). In the MDS plot, the samples…

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Bioconductor – GEOexplorer (development version)

DOI: 10.18129/B9.bioc.GEOexplorer     This is the development version of GEOexplorer; to use it, please install the devel version of Bioconductor. GEOexplorer: an R/Bioconductor package for gene expression analysis and visualisation Bioconductor version: Development (3.14) GEOexplorer is a Shiny app that enables exploratory data analysis and differential gene expression of…

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Row names and probe names does not match in topTable output

Row names and probe names does not match in topTable output 0 Hello I am using limma to analyze differential methylation on a 850k Illumina array, and set up my model as recommended by the user guide. Today I noticed after running topTable() that the rownames in the result data…

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Bioconductor – methylationArrayAnalysis

DOI: 10.18129/B9.bioc.methylationArrayAnalysis     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see methylationArrayAnalysis. A cross-package Bioconductor workflow for analysing methylation array data. Bioconductor version: 3.11 Methylation in the human genome is known to be associated with development and disease. The Illumina Infinium methylation…

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Bioconductor – wateRmelon

DOI: 10.18129/B9.bioc.wateRmelon     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see wateRmelon. Illumina 450 methylation array normalization and metrics Bioconductor version: 3.11 15 flavours of betas and three performance metrics, with methods for objects produced by methylumi and minfi packages. Author: Leonard…

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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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Postdoctoral Scientist in Statistical Bioinformatics and Software Development, WEHI, Melbourne, Australia

Research Officer (Statistical Bioinformatics)Bioinformatics Division, WEHI, Australia An opportunity is available for a Research Officer (Statistical Bioinformatics) to join the Bioinformatics Division at Australia’s pre-eminent biomedical research institute. About the position An exciting opportunity exists for a postdoctoral scientist (Research Officer) to join the research laboratory of Professor Gordon Smyth…

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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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which normalization before differential expression analysis (legacy=TRUE vs. legacy=FALSE)

TCGAbiolinks: which normalization before differential expression analysis (legacy=TRUE vs. legacy=FALSE) 1 Dear All, I am following the TCGAbiolinks tutorial for conducting differential expression analysis on TCGA data (“TCGAanalyze: Analyze data from TCGA” section). I have 2 questions about it. 1) I don’t understand the following: when dealing with legacy=TRUE data…

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LIMMA

LIMMA 0 Guys can I ask do you know if Limma – Voom from Limma is suitable for microarrays? I know it was developed more for RNA seq but since the base technology is Limma which was originally developed for microarrays do you know if Voom is suitable for Microarrays…

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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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Bioconductor Forum

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…

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Extract log2FC values from volcanoplot() possible?

Extract log2FC values from volcanoplot() possible? 1 Hello, An MArrayLM object created with eBayes() from the limma package contains the slot $p.values, which I suppose is used by volcanoplot() to make the volcano plot. Since the volcano plot has log2FC in the x-axis, I suppose volcanoplot() also gets the log2FC…

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Gdcprepare() error.

I’m really struggling with this and I need urgent help. I keep running the following code but after the gdcprepare function, it either crashes my computer or freezes the console. I have no idea what to do, someone please help. library(“TCGAbiolinks”, quietly = T) library(“limma”, quietly = T) library(“edgeR”, quietly…

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Agilent-016436 Human miRNA Microarray 1.0

Upon request, a quick tutorial for processing the Agilent micro-RNA (miRNA) microarray data of GSE28955. The raw TXT files are contained in: ftp.ncbi.nlm.nih.gov/geo/series/GSE28nnn/GSE28955/suppl/GSE28955_RAW.tar Download this TAR file Unpack it [the TAR file] Unzip the txt.gz files Store these [txt files] in a directory raw/ Then, create a tab-delimited file, targets.txt,…

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How to get data from GEO by using getGEO function ?

How to get data from GEO by using getGEO function ? 0 Hello everyone, I am using R package GEOquery to get a geo object from file ( in my directory) by getgeo function. I already download the required packages BiocManager::install(“DESeq2”) BiocManager::install(“limma”) BiocManager::install(“GEOquery”) library(DESeq2) library(limma) library(Biobase) library(GEOquery) I used this…

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Power calculation for microarray data

Power calculation for microarray data 0 I have an initial sample of 228 patients from a microarray study. Recently I have obtained a new set of labels specifying different condition types for only 69 out of the 228 patients. I wanted to run a DEG analysis on this set of…

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Why do I get a big log fold change but small mean change in b value when plotting differential methylation?

Why do I get a big log fold change but small mean change in b value when plotting differential methylation? 0 Hello I am doing differential methylation analysis using limma. I use the m values for testing and b values for plotting. I plotted a volcano plot visualizing the p…

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microarray miRNA expression data analysis

I wrote a script on how to analyze the microarray-based miRNA expression data. Here is my code: # general config baseDir <- ‘.’ annotfile <- ‘mirbase_genelist.tsv’ setwd(baseDir) options(scipen = 99) require(limma) # read in the data targets <- read.csv(“/media/mdrcubuntu/46B85615B8560439/microarray_text_files/targets.txt”, sep=””) # retain information about background via gIsWellAboveBG project <- read.maimages(targets,source=”agilent.median”,green.only…

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Answer: AnnotationHub::mapIds() cannot find existing ENSG (GEO supplemental data cross-r

Hi, a quick check on NCBI Gene reveals that the official symbol for this is *PRXL2C*, not *AAED1*. In this way, I would not have expected `org.Hs.eg.db` (using ‘recent’ annotation) to have it. However, I can see that `EnsDb.Hsapiens.v86` (older version) does [have it]. So, there must have been an…

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