Tag: getGEO

GEO dataset Microarray data analysis help

Hello Everyone , I am new to microarray dataset . I want to do this similar kind of plotting using this same mentioned dataset for a different gene . GEO ID : GSE76008 I have tried GEO2R script : <h6>#</h6> library(GEOquery) library(limma) library(umap) gset <- getGEO(“GSE76008”, GSEMatrix =TRUE, AnnotGPL=TRUE)[1] fvarLabels(gset)…

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Differential Expression Analysis using Bioconductor (RStudio) and GEO2R (GEO)

Hello everyone, I’ve been having the same question for a while now. I’m also conducting my own analysis of differential expression on a microarray dataset in R. However, the data is different from the results obtained using GEO2R. Here’s my line of code: my_id <- “GSE80178” gse <- getGEO(my_id, GSEMatrix…

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How to find OS duration, status information of patients in GSE1159 or GSE6891 (Microarray data analysis)

How to find OS duration, status information of patients in GSE1159 or GSE6891 (Microarray data analysis) 0 Hello. I want to analyze the survival of AML patients in GSE1159 and GSE6891. However, the datasets for these series do not have survival data (OS, status). Many papers have shown survival curves…

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How to find OS duration, status information of patients in GSE1159 (Microarray data analysis)

How to find OS duration, status information of patients in GSE1159 (Microarray data analysis) 0 Hello, many papers showed survival analysis using GSE1159 (N Engl J Med 2004; 350:1617-1628 and etc…). Although I got pData in GSE1159 in R, I didn’t find OS, status of patient infromation. how to get…

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Quality Control – Microarray bioinformatic analyses

Hi, Can someone help me understand the quality control steps. Specifically, I want to know if it filtered the bad probes and what is considered a bad probe? Also I wanted to know what the purpose of the box plots and density plot is? and if you perform quality control…

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Retrieving single-cell dataset from GEO database

Retrieving single-cell dataset from GEO database 1 I want to retrieve the dataset GSE152938 from the GEO database and convert it to a Seurat object. However, my code below returned an empty dataframe. Is the dataset itself empty or did I import the dataset wrongly? gse <- getGEO(“GSE152938”,GSEMatrix=TRUE) eset <-…

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r – GEO Methylation dataset “GSE73303” shows 0 features

I’m working for a project using GEO, in order to analyze some gene expression data. The SuperSeries I am referring to is GSE73304, but I found some problems working on the SubSeries GSE73303. I started my analysis Microarray expression dataset and everything was fine. Now I have to investigate the…

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Download Geo Tar File Automatically From Linux/Unix

Download Geo Tar File Automatically From Linux/Unix 3 Just a note that the GEOquery bioconductor package does this for a living, if you happen to be targeting R for further processing/analysis. See the help for getGEOSuppFiles() and getGEO(). wget -r -nH –cut-dirs=3 ftp.ncbi.nlm.nih.gov/geo/series/GSE39nnn/GSE39977/ The -r option in the wget command…

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illuminaHumanv2.db returning NA for all Illumina probe ID to gene symbol conversion

illuminaHumanv2.db returning NA for all Illumina probe ID to gene symbol conversion 0 I have downloaded a miRNA expression dataset from NCBI GEO (GSE25631) to study differential gene expression and perform other analyses. As mentioned in GEO, this profiling was performed on GPL8179 Illumina Human v2 MicroRNA expression beadchip. Accordingly,…

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normalization – 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 data to perform normalization and my own set of other analyses later on. Accordingly, I downloaded the Series Matrix File (to match the Sample…

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DESeq2 throwing error while normalizing raw microarray expression data due to presence of negative values

I am trying to download and analyze a miRNA expression dataset from NCBI GEO (GSE25631). I specifically want non-normalized data to perform normalization and my own set of other analyses later on. Accordingly, I downloaded the Series Matrix File (to match the Sample IDs with their phenotype) and the non-normalized…

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Bioconductor, how to select a subset of samples in an ExpressionSet?

I’m working on an R script that downloads gene expression data from GEO, through Bioconductor and the getGEO() function. These commands download all the 436 samples of the repository, but I’m only interested in 157 of them. Precisely, I’m interested in handling only the “samples collection:ch1” column with values “”on…

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Dealing with missing (NA) values in my 450K methylation array dataset

I am looking to analyse some pre-processed infinium 450k methylation data (GSE65820) – values have been normalised and undergone QC and removal of batch effects. I have used GEOquery to download the series matrix file GSE65820 <- getGEO(“GSE65820”, GSEMatrix=TRUE) From this I have extracted metadata about the samples using the…

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[BioC] problem with GEOquery

Hi to everybody, i have a little problem with GEOquery .i when I’m trying to download the GSE2841 dataset I encounter the gse <- getGEO(“GSE2841”) try with URL‘ftp.ncbi.nih.gov/pub/geo/data/geo/by_series/GSE2841_family.soft.gz’Error in downloading the.file(myurl, destfile, mode = mode) :impossible to open URL‘ftp.ncbi.nih.gov/pub/geo/data/geo/by_series/GSE2841_family.soft.gz'&#8221; why???????????? Please help me Best regards Dr Alberto GoldoniMedical Genetics UnitS….

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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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Where is genotype calls in this dataset?

Where is genotype calls in this dataset? 0 Hello, I have a dataset from GEO, with ID = GSE20206. I have already checked the dataset using the below code in R: geo.sample <- getGEO(“GSE20206”, GSEMatrix = TRUE) data1 <- geo.sample[[1]] data2 <- geo.sample[[2]] data3 <- geo.sample[[3]] sample_info <- pData(data1) snp_info…

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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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