I am attempting to perform meta-analysis from gene expression omnibus (GEO) data with crossmeta r package in bioconductor
My issue is that when I attempt to download/unzip the GEO raw data with get_raw() function, I face an error demonstrated below (here I am simply attempting analysis from the vignette to troubleshoot)
library(crossmeta) # specify where data will be downloaded data_dir <- file.path(getwd()) # gather all GSEs gse_names <- c("GSE9601", "GSE15069", "GSE50841", "GSE34817", "GSE29689") # gather Illumina GSEs (see 'Checking Raw Illumina Data') illum_names <- c("GSE50841", "GSE34817", "GSE29689") # download raw data get_raw(gse_names, data_dir)
which returns the following for every series in
https://ftp.ncbi.nlm.nih.gov/geo/series/GSE9nnn/GSE9601/suppl/ No supplemental files found. Check URL manually if in doubt https://ftp.ncbi.nlm.nih.gov/geo/series/GSE9nnn/GSE9601/suppl/
This is despite the fact that supplemental files for all of these series (GSEs) do exist. I have attempted this on other series as well to no avail. Any assistance would be much appreciated.
Big thanks in advance!
Additional note: the function
GEOquery package) is used in the source code for
getGEOSuppFiles() works completely fine.