Problem with downloading GSE file by GEOquery
1
0
Entering edit mode
2.3 years ago
Kim ▴ 10

Hello everyone

I'm learning to use GEOquery to analyze data from GEO. I can download GSM, GPL and GDS files from GEO with no problems, but I can't download GSE files.

The code I use: gse <- getGEO("GSE42657", destdir=".")

The returned message: Error in open.connection(x, "rb") : Timeout was reached: Connection timed out after 10015 milliseconds

Could you please tell me what happened and how to fix it?

Thank you very much

GEOquery download timeout GSE file • 2.4k views
ADD COMMENT
0
Entering edit mode

Thank Matthew. I've just tried your solution but using download.file command to download the file instead. Then I tried to open the file in R by getGEO but it's just running (nearly 1h already) without successfully opening the GSE file. Do you have any idea about this?

ADD REPLY
0
Entering edit mode

Everything is solved. I downloaded the file directly from the website and loaded it in R and now it works. Thank you very much for your solution.

ADD REPLY
0
Entering edit mode

If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one if they work.
Upvote|Bookmark|Accept

ADD REPLY
5
Entering edit mode
2.3 years ago
MatthewP ★ 1.0k

Hello, this may be connetion issue(happen often using GEOquery). One solution is download the Series Matrix File byhand. For example in your case

# download Matrix file
wget ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE42nnn/GSE42657/matrix/

# then in R
gse <- getGEO(filename="/yourpath/GSE42657_series_matrix.txt.gz", AnnotGPL=TRUE)
ADD COMMENT

Login before adding your answer.

Traffic: 2063 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6