This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Problem in retrieving geo data sets

I am trying to retrieve geodata sets "GSE146049" through the following commands:

#Creation of object(folder) exdir
exdir <- path.expand("~/GSE146049_RAW")
dir.create(exdir, showWarnings = FALSE)

URL < -"https://ftp.ncbi.nlm.nih.gov/geo/series/GSE146nnn/GSE146049/suppl/GSE146049_RAW.tar"
FILE <- file.path(tempdir(), basename(URL))

#Downlaod the Raw Data from GEO
utils::download.file(URL, FILE, mode = "wb")

But its throws the following errors:

Warning message in utils::download.file(URL, FILE, mode = "wb"):
"URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE146nnn/GSE146049/suppl/GSE146049_RAW.tar': status was 'Couldn't resolve host name'"
Error in utils::download.file(URL, FILE, mode = "wb"): cannot open URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE146nnn/GSE146049/suppl/GSE146049_RAW.tar'
Traceback:

1. utils::download.file(URL, FILE, mode = "wb")

How can I solve this issue? I want to get raw counts and then convert them by using TMM normalization

geo
• 1,477 views • link
written by anasjamshed anasjamshed

This must be some local issue. That URL works. Did you try it in a browser?

• 0 views • link
written by GenoMax GenoMax

is i working on your side? I am using jupyter notebook

• 0 views • link
written by anasjamshed anasjamshed

Yes it gets about a 28 Mb file.

• 0 views • link
written by GenoMax GenoMax

can you show me the screenshot?

• 0 views • link
written by anasjamshed anasjamshed

0 answers

No answers yet.

Log in to answer this question.

More posts like this