Tag: GEOquery

Identification of key genes related to immune infiltration in cirrhosis via bioinformatics analysis

Lozano, R. et al. Global and regional mortality from 235 causes of death for 20 age groups in 1990 and 2010: a systematic analysis for the Global Burden of Disease Study 2010. Lancet 380(9859), 2095–2128 (2012). Google Scholar  Blachier, M., Leleu, H., Peck-Radosavljevic, M., Valla, D. C. & Roudot-Thoraval, F….

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microarray analysis – gene upregulation/downregulation

microarray analysis – gene upregulation/downregulation 0 Hi guys, I have performed microarray differential expression analysis using the following R commands/script: library(“arrayQualityMetrics”) > library(GEOquery) > library(oligo) > library(Biobase) > library(affy) > library(“splitstackshape”) > library(“tidyr”) > library(dplyr) > celFiles <- list.celfiles() > affyRaw <- read.celfiles(celFiles) Platform design info loaded. Reading in :…

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Microarray DEG scatterplot

Hi, I have found that my selected gene, probe I.D 201667_at is differentially expressed between WDLPS and DDLPS tumour tissue samples after performing microarray DEG analysis. Instead of just a p value in a table format: Probe I.D “201667_at” logFC 10.8205874181535 AveExpr 10.6925705768407 t 82.8808890739766 P.Value 3.10189446528995e-88 adj.P Val 3.10189446528995e-88…

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Acute phase of ischemia-reperfusion in rats

Introduction Stroke is one of the leading causes of death and disability worldwide, which causes substantial economic and social burdens.1 Ischemic stroke is caused by insufficient blood and oxygen supply to the brain,2 accounting for about 85% of the casualties of stroke patients.3 The concept of treatment for ischemic injury…

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Error in SummarizedExperiment

I have installed DESeq2 version 1.36.0 samples <- colnames(txi$counts) group <- as.factor(c(“control”,”control”,”control”,”control”,”control”,”diet”,”diet”,”diet”,”diet”,”diet”, “control”,”control”,”control”,”control”,”control”,”diet”,”diet”,”diet”,”diet”,”diet”,”diet”)) coldata <- data.frame(samples, group, stringsAsFactors = F) coldata <- coldata[,c(“samples”,”group”)] coldata$samples <- factor(coldata$samples) coldata$group <- factor(coldata$group) rownames(coldata) <- sub(“fb”, “”, rownames(coldata)) all(rownames(coldata$samples) %in% colnames(txi)) all(rownames(coldata) == colnames(txi)) TRUE library(DESeq2) ddsTxi <- DESeqDataSetFromTximport(txi, colData = coldata, design =…

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GPL arguments in getGEO()

GPL arguments in getGEO() 0 Hi, I’ve been trying to get GEO data using the getGEO() function and I was wondering what do the arguments AnnotGPL and getGPL do exactly? I tried setting them to T or F and then comparing the output but I don’t observe any differences, am…

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data object isn’t of a recognized data class

R error : Error in getEAWP(object) : data object isn’t of a recognized data class 0 I get this error in microarray analysis > fit = lmFit(DataSeries, design) Error in getEAWP(object) : data object isn’t of a recognized data class microarray GEOquery • 41 views Login before adding your answer….

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unable to find an inherited method for function ‘exprs’ for signature ‘”list”’

R error: unable to find an inherited method for function ‘exprs’ for signature ‘”list”’ 1 Hi I get this error in exprs >DataSeries = getGEO(“GSE5847”, GSEMatrix = T, AnnotGPL = T, destdir = “D:/Microarray Data/sharifi.data” ) >expressionData = exprs(DataSeries) >Error in (function (classes, fdef, mtable) : unable to find an…

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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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AnnotationHub::mapIds() cannot find existing ENSG (GEO supplemental data cross-referenced with ensembl.org)

Anyone know why I’m not getting ENSG ids for some of these symbols? The example below retrieves `NA` for multiple symbols, including AAED1 [whose ENSG is ENSG00000158122][1]. “` > library(AnnotationHub) > library(org.Hs.eg.db) > library(GEOquery) > temp download.file(getGEO(“GSM4430459″)@header$supplementary_file_1,temp) > genes unlink(temp) > ensids = mapIds(org.Hs.eg.db, keys=genes, column=”ENSEMBL”, keytype=”SYMBOL”, multiVals=”first”) > ensids[“AAED1”]…

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