Trouble using get_raw() function in crossmeta R package to extract GEO data for differential expression analysis
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Entering edit mode
13 months ago

Hello,

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)

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")

get_raw(gse_names, data_dir)


which returns the following for every series in gse_names:

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.

Additional note: the function getGEOSuppFiles (from GEOquery package) is used in the source code for get_raw() and getGEOSuppFiles() works completely fine.

R crossmeta meta-analysis gene-expression • 397 views
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Entering edit mode

Exactly, same problem I am facing. Anybody's help would be much appreciated