Tag: getGEO

[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….

Continue Reading [BioC] problem with GEOquery

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…

Continue Reading GPL arguments in getGEO()

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…

Continue Reading Where is genotype calls in this dataset?

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…

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

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…

Continue Reading How to get data from GEO by using getGEO function ?

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”]…

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