Question: Problem with downloading GSE file by GEOquery
0
gravatar for Kim
4 months ago by
Kim0
Kim0 wrote:

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

ADD COMMENTlink modified 4 months ago • written 4 months ago by Kim0

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 REPLYlink written 4 months ago by Kim0

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 REPLYlink written 4 months ago by Kim0

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 REPLYlink written 4 months ago by genomax75k
5
gravatar for MatthewP
4 months ago by
MatthewP330
China
MatthewP330 wrote:

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 COMMENTlink written 4 months ago by MatthewP330
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