Problem in retrieving geo data sets
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15 months ago
anasjamshed ▴ 120

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

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

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Yes it gets about a 28 Mb file.

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can you show me the screenshot?

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