Tag: getGEO

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…

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,…

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…

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…

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…

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…

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….

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…

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…

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…

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…

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”]…